Re: [gmx-users] pdb2gmx command not found

Versions of GROMACS for awhile now have moved all the scripts underneath "gmx". So now you need use "gmx pdb2gmx" On Fri, 20 Mar. 2020, 5:28 am Sutanu L'Étranger, < schrodingerscat...@gmail.com> wrote: > Hi, > > I've recently installed gromacs latest version, but when I type pdb2gmx, it > shows "

[gmx-users] Parrinello-Rahman and Pairtype1 causing pressure instabilities

Hello, I hope this message finds you well! I'm running a pretty simple simulation of a polyethylene melt (N = 100, 50 chains in the simulation, T = 500K, P = 1atm, NPT ensemble, dt = 1 fs, OPLS-AA FF). My simulations are exhibiting large, unstable volume fluctuations when I use the combination of

Re: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1

>This sounds very much like something we should >fix. Can you file a bug report >at >https://redmine.gromacs.org/ where you can also >upload the file that you >are trying to run? Let me >know if you have any trouble with uploading the >>report - I'm eager to know what happened. Best, >Christian

Re: [gmx-users] Problem in protein ligand interaction

Hi Cristina, Previous ultra-long conventional molecular dynamics works have shown that ligand can find its binding pocket and finally bind in a crystal complex pose. Also enhance sampling techniques, e.g. metadynamics, can speeed the binding process. So, if you want ligand to find its bindin

Re: [gmx-users] ERROR 1 [file lig.itp, line 575]:: ; Duplicate atom index (19) in virtual_sites3

On 3/19/20 1:25 PM, Adarsh V. K. wrote: Dear all, How to overcome this error ? ( ERROR 1 [file lig.itp, line 575]; Duplicate atom index (19) in virtual_sites3) I tried after deleting the line which returned an error message but still the problem does not get resolved. Command line: *gmx grom

Re: [gmx-users] 2020.1: comm broken with -update gpu -bonded gpu ?

On 3/19/20 1:01 PM, Jochen Hub wrote: Hi developers, I am running a simple DPPC membrane (Berger force field, PME, 1nm cutoff, 4fs time step, all standard) with 2020.1 and comm-mode    = Linear nstcomm  = 100 comm-grps    = DPPC water  ; OR System bu

Re: [gmx-users] distance restraints between different chains

I think pulling code can solve the problem, http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#com-pulling On Fri, Mar 20, 2020 at 12:04 PM Oscar Hernandez Alba wrote: > Dear all, > > > > I am trying to run MD with a protein with four different chains. When > I > co

[gmx-users] distance restraints between different chains

Dear all, I am trying to run MD with a protein with four different chains. When I convert this structure to gromacs, I have four different molecules in the topology file. I would like to use distance restraints between specific atoms of different chains. I have created the itp file with t

Re: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1

Hi Yujie, This sounds very much like something we should fix. Can you file a bug report at https://redmine.gromacs.org/ where you can also upload the file that you are trying to run? Let me know if you have any trouble with uploading the report - I'm eager to know what happened. Best, Chr

Re: [gmx-users] gmx do_dssp not work for gromacs 2020 or 2020.1

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[gmx-users] Problem in protein ligand interaction

Dear Gromacs users, I'm trying to simulate a protein-lipid interaction. Analyzing the simulation, it seems that the lipid does't have enough driving force to reach the binding pocket, since van der Waals forces move the lipind towards the binding pocket whereas electrostatics move the lipid in