# General Topics in Molecular Dynamics **URL:** https://ask.bioexcel.eu/c/general-topics-in-molecular-dynamics/19.md [Latest](https://ask.bioexcel.eu/latest.md) · [Categories](https://ask.bioexcel.eu/categories.md) · [Tags](https://ask.bioexcel.eu/tags.md) --- ## [About General Topics in Molecular Dynamics](https://ask.bioexcel.eu/t/about-general-topics-in-molecular-dynamics/1555)
**Author:** [@cblau](https://ask.bioexcel.eu/u/cblau)\ **Replies:** 0
General musings about molecular dynamics that do not relate directly to GROMACS, HADDOCK or CPMD --- ## [Missing residues on a protein](https://ask.bioexcel.eu/t/missing-residues-on-a-protein/6071)
**Author:** [@Pietro](https://ask.bioexcel.eu/u/Pietro)\ **Replies:** 0\ **Last updated:** [April 13, 2026, 9:40am UTC](https://ask.bioexcel.eu/t/missing-residues-on-a-protein/6071 "2026-04-13T09:40:27Z")
Hello! Prior to use GROMACS to simply perform a quick energy minimization on my protein, I used MODELLER to reconstruct some missing loops. Is that correct or i shouldn’t have spent that much time modelling the missing … --- ## [Using \`martinize2\` to get GōMartini coarse-grained protein parameters (Martini 3)](https://ask.bioexcel.eu/t/using-martinize2-to-get-gomartini-coarse-grained-protein-parameters-martini-3/6040)
**Author:** [@dheeraj.prakaash](https://ask.bioexcel.eu/u/dheeraj.prakaash)\ **Replies:** 0\ **Last updated:** [March 18, 2026, 3:08am UTC](https://ask.bioexcel.eu/t/using-martinize2-to-get-gomartini-coarse-grained-protein-parameters-martini-3/6040 "2026-03-18T03:08:58Z")
Hi all, After using martinize2 to successfully obtain Martini 3 coarse-grained (CG) protein structures a couple of years ago, I have recently been attempting the same, this time aiming to obtain GōMartini parameters rat… --- ## [GROMACS Domain Decomposition Errors in Protein-Membrane Simulation with Martini](https://ask.bioexcel.eu/t/gromacs-domain-decomposition-errors-in-protein-membrane-simulation-with-martini/5452)
**Author:** [@mpapadourakis](https://ask.bioexcel.eu/u/mpapadourakis)\ **Replies:** 0\ **Last updated:** [March 5, 2025, 10:13am UTC](https://ask.bioexcel.eu/t/gromacs-domain-decomposition-errors-in-protein-membrane-simulation-with-martini/5452 "2025-03-05T10:13:48Z")
Hi all, I am attempting to simulate a protein-membrane system (60x60x25) using GROMACS 2024.4 with the Martini3 force field in the NPT ensemble. However, I am encountering domain decomposition errors immediately after m… --- ## [RESP for a cofactor](https://ask.bioexcel.eu/t/resp-for-a-cofactor/4212)
**Author:** [@v.sheg](https://ask.bioexcel.eu/u/v.sheg)\ **Replies:** 0\ **Last updated:** [March 22, 2023, 12:38pm UTC](https://ask.bioexcel.eu/t/resp-for-a-cofactor/4212 "2023-03-22T12:38:04Z")
Hello, I want to ask you for advice. I need to do RESP on a protein cofactor. The cofactor is strongly bound to the protein, so I am trying to decide which conformations I should use to perform charge fitting. Should I … --- ## [Membrane protein constant pH Amber](https://ask.bioexcel.eu/t/membrane-protein-constant-ph-amber/4072)
**Author:** [@mhk](https://ask.bioexcel.eu/u/mhk)\ **Replies:** 1\ **Last updated:** [January 13, 2023, 7:53am UTC](https://ask.bioexcel.eu/t/membrane-protein-constant-ph-amber/4072 "2023-01-13T07:53:13Z")
Hi! I want to use “biobb\_amber\_CpHMD\_notebook”, to prepare my system which is an ion channel for running CpHMD with Amber. My questions are: Is it possible to embed the protein in membrane with biobb in some step? or… --- ## [RNA structure simulation through Gromacs](https://ask.bioexcel.eu/t/rna-structure-simulation-through-gromacs/4039)
**Author:** [@attaka](https://ask.bioexcel.eu/u/attaka)\ **Replies:** 1\ **Last updated:** [January 12, 2023, 3:48am UTC](https://ask.bioexcel.eu/t/rna-structure-simulation-through-gromacs/4039 "2023-01-12T03:48:28Z")
Hello Everyone!! I am working on RNA structure simulation but I got an error on first step to create topology file through this command “gmx pdb2gmx -f S\_000001.pdb -o S\_00000\_proc.gro -ignh” its showing FATAL error: F… --- ## [Parameterisation of Metallo-protein with amber?](https://ask.bioexcel.eu/t/parameterisation-of-metallo-protein-with-amber/3691)
**Author:** [@adanazumi](https://ask.bioexcel.eu/u/adanazumi)\ **Replies:** 4\ **Last updated:** [April 30, 2022, 12:48pm UTC](https://ask.bioexcel.eu/t/parameterisation-of-metallo-protein-with-amber/3691 "2022-04-30T12:48:30Z")
Can someone please help me with a protocol for parameterizing a metallo-protein for MD simulation with amber forcefield? My protein has two FE molecules and the I tried using either frcmod.ionsjc\_tip3p or frcmod.ions234l… --- ## [Amber Sander on GPU](https://ask.bioexcel.eu/t/amber-sander-on-gpu/3687)
**Author:** [@Varbiobbmou](https://ask.bioexcel.eu/u/Varbiobbmou)\ **Replies:** 1\ **Last updated:** [April 25, 2022, 1:37pm UTC](https://ask.bioexcel.eu/t/amber-sander-on-gpu/3687 "2022-04-25T13:37:17Z")
Is Sander in the amber wrapper GPU enabled? If yes, on the protein-ligand complex tutorial how do I get it to use GPUs on my workstation? --- ## [Error in loading parameters for tleap](https://ask.bioexcel.eu/t/error-in-loading-parameters-for-tleap/3160)
**Author:** [@khhel100](https://ask.bioexcel.eu/u/khhel100)\ **Replies:** 0\ **Last updated:** [July 13, 2021, 8:00am UTC](https://ask.bioexcel.eu/t/error-in-loading-parameters-for-tleap/3160 "2021-07-13T08:00:20Z")
error: Error! For atom (.R\.A\) could not find vdW (or other) parameters for type (O.3) my build.leap file: source leaprc.protein.ff14SB source leaprc.water.tip3p source leaprc.gaff source leaprc.lipi… --- ## [Fatal Error in Ligand](https://ask.bioexcel.eu/t/fatal-error-in-ligand/2857)
**Author:** [@imamsamodra](https://ask.bioexcel.eu/u/imamsamodra)\ **Replies:** 1\ **Last updated:** [March 22, 2021, 5:12pm UTC](https://ask.bioexcel.eu/t/fatal-error-in-ligand/2857 "2021-03-22T17:12:57Z")
Hi everyone, I’m have a some problem when I try to run parameterization using Amber. here the log file: ------- .R\.A\ and .R\.A\ FATAL: Atom .R\.A\ does not have a type. FATAL:… --- ## [Cgenff\_charmm2gmx error](https://ask.bioexcel.eu/t/cgenff-charmm2gmx-error/2781)
**Author:** [@mohammad](https://ask.bioexcel.eu/u/mohammad)\ **Replies:** 0\ **Last updated:** [January 18, 2021, 9:15pm UTC](https://ask.bioexcel.eu/t/cgenff-charmm2gmx-error/2781 "2021-01-18T21:15:27Z")
Hi. I try to convert cgenff server output by cgenff\_charmm2gmx for gromacs but get an error. I use from gromacs 2020.4 in ubuntu 20.04. I installed networkx 2.3 and a newer version of python. In addition, numpy was insta… --- ## [Visualising Chain B center of mass](https://ask.bioexcel.eu/t/visualising-chain-b-center-of-mass/2775)
**Author:** [@Kris](https://ask.bioexcel.eu/u/Kris)\ **Replies:** 0\ **Last updated:** [January 10, 2021, 3:16pm UTC](https://ask.bioexcel.eu/t/visualising-chain-b-center-of-mass/2775 "2021-01-10T15:16:05Z")
Hi all, This is a bit of a generic question to do with displaying the results of ab initio docking. I have 200 complexes as determined by ab initio docking with HADDOCK2.4 and I’ve added all of these to PyMOL (in one w… --- ## [Benchmark set suggestions for GROMACS](https://ask.bioexcel.eu/t/benchmark-set-suggestions-for-gromacs/2377)
**Author:** [@busrasavas](https://ask.bioexcel.eu/u/busrasavas)\ **Replies:** 0\ **Last updated:** [August 4, 2020, 2:58pm UTC](https://ask.bioexcel.eu/t/benchmark-set-suggestions-for-gromacs/2377 "2020-08-04T14:58:31Z")
Dear all, We would like to carry out a GROMACS performance test on our local resources. Would you have any recommendation for a benchmark set to be used for this purpose? Thanks in advance --- ## [Effect of using Na or K for MD Simulations](https://ask.bioexcel.eu/t/effect-of-using-na-or-k-for-md-simulations/2304)
**Author:** [@busrasavas](https://ask.bioexcel.eu/u/busrasavas)\ **Replies:** 1\ **Last updated:** [July 5, 2020, 12:39pm UTC](https://ask.bioexcel.eu/t/effect-of-using-na-or-k-for-md-simulations/2304 "2020-07-05T12:39:29Z")
Dear All, I am working on a Protein-DNA complex. I run my simulations with Amber14sb-PARMbsc1 force field. We performed couple of simulations to see the difference of using different ions (e.g. Na and K). As can be seen… --- ## [Amber99sb-disp (ff for disordered and ordered proteins)](https://ask.bioexcel.eu/t/amber99sb-disp-ff-for-disordered-and-ordered-proteins/2245)
**Author:** [@daniele.montepietra](https://ask.bioexcel.eu/u/daniele.montepietra)\ **Replies:** 0\ **Last updated:** [June 23, 2020, 3:28pm UTC](https://ask.bioexcel.eu/t/amber99sb-disp-ff-for-disordered-and-ordered-proteins/2245 "2020-06-23T15:28:29Z")
Hi there! I’m running simulation of a protein containing extended intrinsically disordered regions. I want to use the amber99sb-disp force fiels, that is the state of the art force field for intrinsically disordered pro… --- ## [Trajectory and Topology files](https://ask.bioexcel.eu/t/trajectory-and-topology-files/1170)
**Author:** [@duttaa19](https://ask.bioexcel.eu/u/duttaa19)\ **Replies:** 0\ **Last updated:** [September 11, 2018, 6:52am UTC](https://ask.bioexcel.eu/t/trajectory-and-topology-files/1170 "2018-09-11T06:52:43Z")
What are Trajectory and Topology files?? Also I am not able to view the figures though JAVA is installed in my PC… Pl. help --- ## [Follow up on Webinar: "NAFlex, a web server for the study of nucleic acid flexibility" by Federica Battistini (2017-07-20)](https://ask.bioexcel.eu/t/follow-up-on-webinar-naflex-a-web-server-for-the-study-of-nucleic-acid-flexibility-by-federica-battistini-2017-07-20/412)
**Author:** [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)\ **Replies:** 0\ **Last updated:** [July 18, 2017, 8:30am UTC](https://ask.bioexcel.eu/t/follow-up-on-webinar-naflex-a-web-server-for-the-study-of-nucleic-acid-flexibility-by-federica-battistini-2017-07-20/412 "2017-07-18T08:30:49Z")
Feel free to add here any comments or questions from the “NAFlex, a web server for the study of nucleic acid flexibility" webinar by Federica Battistini (2017-07-20). NAFlex web server If you want to be updated on the… --- ## [Simulation time for Protein System](https://ask.bioexcel.eu/t/simulation-time-for-protein-system/1554)
**Author:** [@nashit](https://ask.bioexcel.eu/u/nashit)\ **Replies:** 1\ **Last updated:** [May 6, 2019, 1:03pm UTC](https://ask.bioexcel.eu/t/simulation-time-for-protein-system/1554 "2019-05-06T13:03:47Z")
What is sufficient time for simulating a large protein system like Kinesin Motors ? What are the parameters that decide the simulation time is enough. I have heard simulation time is almost 100 ns for bigger protein sys…