[gmx-users] -sep option

Dear colleagues, How should I use -sep option to convert a frame of a trajectory to pdb? Can anyone send me the command line? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Hamiltonian replica exchange in gromacs 4.6.7

Hi, You certainly want the code to take the path where lambda varies, but if you comment out the check for unequal lambda and avoid the check that T is unequal, things should work fine. Mark On Thu, Mar 8, 2018 at 2:59 AM Carlo Martinotti < carlo.martino...@postgrad.curtin.edu.au> wrote: >

Re: [gmx-users] Calculation of potential of mean force between sodium and chloride ion pair in water using replica exchange umbrella sampling in gromacs

Hi, Just out of curiosity, what is the point of REMD for such a simple system? Is the enhanced sampling really worth the overhead? Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala

Re: [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?

Hi, Yes, if you check out the documentation of tabulated non-bonded interactions in the reference manual, you will see that you can apply different tables for particles when drawn from different energy groups. Mark On Sat, Mar 10, 2018 at 1:06 AM Debdas Dhabal wrote: >

Re: [gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?

Dear Mark, Thanks so much for your prompt reply. I had gone through that manual and I was able to use two different non-bonded potential for two different energy groups using table potential. But my question is a bit different. May be I was not able to make my question clear. I know the fact

Re: [gmx-users] Gromacs Tutorial by Justin

On 3/10/18 1:24 PM, Faezeh Pousaneh wrote: Dear Justin One more question please, Do we need to have constraint in this model of CO2? Isn't it so that we have fixed the bond lengths and angles (180) in the topology by this method? The molecule behaves as a rigid rotor. The math is all laid

[gmx-users] Comm-mode

Dear Gromacs people, I have a question please. In which condition we must use center of mass removal? Is that optional or necessary? and how to know which mode (linear or angular) is better for our simulations? Many thanks -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] -sep option

Dear justin, I want to make pdb files with regular intervals from a long trajectory.Can you please tell me an example command line using -sep? I want to get 100 pdbs from a 100 ns trajectory with 1ns (1000 ps) intervals.  Sent from Yahoo Mail on Android On Sat, Mar 10, 2018 at 20:56,

Re: [gmx-users] -sep option

On 3/10/18 9:18 AM, Mansoureh Shahbazi wrote: Dear colleagues, How should I use -sep option to convert a frame of a trajectory to pdb? Can anyone send me the command line? Thanks The -sep option is used to write a given interval of a trajectory into separate files. If you just want a

Re: [gmx-users] Comm-mode

On 3/10/18 12:17 PM, Amin Rouy wrote: Dear Gromacs people, I have a question please. In which condition we must use center of mass removal? Is that optional or necessary? Typically necessary. and how to know which mode (linear or angular) is better for our simulations? Linear is only

Re: [gmx-users] Comm-mode

thank you so much. On Sat, Mar 10, 2018 at 6:33 PM, Justin Lemkul wrote: > > > On 3/10/18 12:31 PM, Amin Rouy wrote: > >> Thank you Justin. >> What if we do not know the phase of the final result? of if we are in 2 >> phase region (gas-liquid) >> > > If you're applying PBC you

Re: [gmx-users] Gromacs Tutorial by Justin

Dear Justin One more question please, Do we need to have constraint in this model of CO2? Isn't it so that we have fixed the bond lengths and angles (180) in the topology by this method? I run 2 simulations, one with constraints = all-angles and the other with constraints = all-bonds, I get

Re: [gmx-users] Comm-mode

Thank you Justin. What if we do not know the phase of the final result? of if we are in 2 phase region (gas-liquid) On Sat, Mar 10, 2018 at 6:25 PM, Justin Lemkul wrote: > > > On 3/10/18 12:17 PM, Amin Rouy wrote: > >> Dear Gromacs people, >> >> I have a question please. >> >>

Re: [gmx-users] Comm-mode

On 3/10/18 12:31 PM, Amin Rouy wrote: Thank you Justin. What if we do not know the phase of the final result? of if we are in 2 phase region (gas-liquid) If you're applying PBC you have to use linear as your comm-mode (grompp will fail otherwise, so that's a pretty good hint). -Justin