[gmx-users] Stochastic dynamics (sd)

Dear all, I used the Stochastic dynamics (sd) integrator for single molecule in gas phase for around 80 ns (I need this for bonding parameter course-grained particularization using votca), would you please have a look at the sturcure before and after SD, and help me underestand why this happens?

Re: [gmx-users] Possible to extract gro file from a tpr?

Just say No! :-) On Fri, Mar 30, 2018, 19:58 Alex wrote: > Or, and that is a very peculiar option, genion with -conc 0. :) > > Alex > > > On 3/30/2018 4:28 AM, Justin Lemkul wrote: > > On Fri, Mar 30, 2018 at 5:38 AM Viveca Lindahl > > wrote: > > >

Re: [gmx-users] Possible to extract gro file from a tpr?

Or, and that is a very peculiar option, genion with -conc 0. :) Alex On 3/30/2018 4:28 AM, Justin Lemkul wrote: On Fri, Mar 30, 2018 at 5:38 AM Viveca Lindahl wrote: Hi users, Is it possible to extract a gro file from a tpr? Unfortunately 'gmx mdrun -nsteps 0'

[gmx-users] ss.xpm file: chain separator location? first residue showing first, or last residue showing first?

Dear Gromacs, (Sorry I post this again as I have not got confirmed answer yet) In the ss.xpm file for secondary structures, can I ask if the first residue shows first, or last residue shows first? I could not find the description in the file. I also have a chain separator. Can I ask does it

Re: [gmx-users] gmx check precision

On 3/30/18 7:29 AM, jt555 wrote: Hello there, I am currently using GROMACS version 5.1.2 and had a question in relation to the gmx check command. The following appears on the screen after invocation of gmx check -f protein.pdb: GROMACS: gmx check, VERSION 5.1.2 Executable:

[gmx-users] gmx check precision

Hello there, I am currently using GROMACS version 5.1.2 and had a question in relation to the gmx check command. The following appears on the screen after invocation of gmx check -f protein.pdb: GROMACS: gmx check, VERSION 5.1.2 Executable: /usr/bin/gmx Data prefix: /usr Command line:

Re: [gmx-users] Possible to extract gro file from a tpr?

On Fri, Mar 30, 2018 at 5:38 AM Viveca Lindahl wrote: > Hi users, > > Is it possible to extract a gro file from a tpr? Unfortunately 'gmx mdrun > -nsteps 0' does not give a confout.gro :) > Just use editconf. -Justin > -- > Viveca > -- > Gromacs Users mailing list >

Re: [gmx-users] Possible to extract gro file from a tpr?

Hi Viveca, You could specify in trjconv to output a gro file: gmx trjconv -s md.tpr -f md.xtc -o md.gro ... Would that work? Gregory Get Outlook for Android From: Viveca Lindahl Sent: Friday, March 30, 5:38 AM Subject: [gmx-users] Possible to extract gro file from a

[gmx-users] Possible to extract gro file from a tpr?

Hi users, Is it possible to extract a gro file from a tpr? Unfortunately 'gmx mdrun -nsteps 0' does not give a confout.gro :) -- Viveca -- 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