[gmx-users] Continuing a simulation

scratch because I had expected it to show me step from wherever it exited last and continue from there on. Would really appreciate if anyone could guide me further. -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

[gmx-users] Re: Continuing a simulation plus another error

Hi again, Sorry for the repetition in email. When I ran the mdrun command, I got an error of "Attempting to read a checkpoint file of version 13 with code of version 12" Can anyone please help me with this error too? On Mon, Dec 24, 2012 at 4:35 PM, Ankita naithani wrote: >

Re: [gmx-users] Re: Continuing a simulation plus another error

on, Dec 24, 2012 at 5:28 PM, Justin Lemkul wrote: > > > On 12/24/12 11:54 AM, Ankita naithani wrote: >> >> Hi again, >> >> Sorry for the repetition in email. >> >> When I ran the mdrun command, I got an error of >> >> "Attempting to read a ch

Re: [gmx-users] MM-GB/SA analysis in Gromacs

www.linkedin.com/in/andreaspitaleri > - > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Ma

Re: [gmx-users] rmsf analysis

se don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/ma

Re: [gmx-users] Re: rmsf analysis

iling_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ankita Naithani -- gmx-users mailing li

[gmx-users] Protein - Ligand tetramer simulation

would really appreciate any help in this matter. Best Wishes, -- Ankita Naithani -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromac

Re: [gmx-users] Protein - Ligand tetramer simulation

Hi Justin, Thank you so much for a swift response. I will try as suggested and get back to you with my hurdles. Appreciate the help! Best Wishes, Ankita On Thu, Aug 9, 2012 at 4:09 PM, Justin Lemkul wrote: > > > On 8/9/12 10:40 AM, Ankita naithani wrote: >> >> Hi all,

[gmx-users] Protein-ligand - genion error

as to what exactly and how I need to incorporate the changes. Also, the co-ordinate file, should the changes be made to the one obtained after running the genbox step? Best Wishes, -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

Re: [gmx-users] Protein-ligand - genion error

ligands i.e. FDP,ATP and OXL but subsequently, I find that only FDP is present in these files and not ATP and OXL. Please, could help me with both my problems. On Fri, Aug 10, 2012 at 6:08 PM, Justin Lemkul wrote: > > > On 8/10/12 1:05 PM, Ankita naithani wrote: >> >> D

Re: [gmx-users] Protein-ligand - genion error

Hi Justin, Thank you so much for your reply. It really helped me a lot. I think I have managed to clear this step. Thanks once again. Best Wishes, On Fri, Aug 10, 2012 at 6:30 PM, Justin Lemkul wrote: > > > On 8/10/12 1:26 PM, Ankita naithani wrote: >> >> Hi Justin, >

[gmx-users] Ions topology

, -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subs

Re: [gmx-users] Ions topology

Dear Mark, Thank you for your reply. I am using gromos53a6 force field. On Tue, Aug 14, 2012 at 11:16 AM, Mark Abraham wrote: > On 14/08/2012 7:45 PM, Ankita naithani wrote: >> >> Dear All, >> >> I wanted to ask that from where can I get the topologies and >> c

[gmx-users] Topology file

l the individual chains. Do I need to add in them manually? Also, I am unable to understand as to why did it not get included in the first instance itself? I am using gromos53a6 force field. Best Wishes, -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

[gmx-users] Re: Topology file

Is this because the topol_Protein_Chain_D.itp has a line of including the position restraint file for chain D? On Wed, Aug 15, 2012 at 2:05 PM, Ankita naithani wrote: > Hi, > > I noticed that in my topology file, there is no inclusion of position > restraint file for my protein.

[gmx-users] NPT Equilibration error

a random seed Could you please guide me to solve the problem? -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support

[gmx-users] g_confrms

about using g_confrms irrespective of the number of atoms. Best Wishes, -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting

Re: [gmx-users] g_confrms

n for the difference? On Sun, Sep 16, 2012 at 3:03 PM, Mark Abraham wrote: > On 16/09/2012 11:49 PM, Ankita naithani wrote: >> >> Hi, >> >> I am trying to use g_confrms to compare my initial and final structure >> and fit them on their backbone. However, I notice

Re: [gmx-users] TIP4P water model

>> > > The problem is occurring with grompp before genion. We would need to see > all the prior commands (exactly copied and pasted from the terminal) as well > as the [molecules] section of the topology, to at least start to guess at > what's wrong. It is unusual to find a fa

[gmx-users] Snapshot and co-ordinate query

if you could kindly guide me towards these queries. Kind regards -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please

Re: [gmx-users] Snapshot and co-ordinate query

Hi Justin, Thank you so much for the clarification. Kind regards, Ankita On Wed, Jun 5, 2013 at 11:28 PM, Justin Lemkul wrote: > > > On 6/5/13 3:03 PM, Ankita naithani wrote: > >> Hi, >> >> I have two questions. >> >> I have performed a simula

[gmx-users] Eigenvector and eigenvalues

exed about the problem. I am sorry for this extremely long and confusing post, but any help in this regard would be really beneficial. Kind regards, Ankita -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search t

Fwd: [gmx-users] Eigenvector and eigenvalues

> Hi Ankita, >> >> Please provide the commands you've run and the screen output from g_covar. >> >> Cheers, >> >> Tsjerk >> >> >> >> On Thu, Jun 6, 2013 at 3:44 PM, Ankita naithani > >wrote: >> >> > Hi, >&g

Re: [gmx-users] Eigenvector and eigenvalues

x operation, using > the matrix of selected eigenvectors and the corresponding atoms of the > trajectory. Because the matrix of eigenvectors is derived from C-alpha > atoms only in your case, it is not possible to get anything else out of it. > > Hope it helps, > > Tsjerk >

[gmx-users] Covariance file format

atoms. It would be really helpful if someone could explain the file format. Kind regards, Ankita -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support

[gmx-users] Re: Covariance file format

I can use the eigenvectors Kind regards Ankita On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > Hi Ankita, > > The fie contains the eigenvectors as > > x1 y1 z1 > x2 y2 z2 > ... > xN yN zN > > Hope it helps, > > Tsjerk > > > On Mon, Jul 1, 2013

[gmx-users] Re: Covariance file format

m x1y1 1/n sum x1z1 > 1/n sum x1x2 1/n sum x1y2 1/n sum x1z2 > ... > 1/n sum zNxN 1/n sum zNyN 1/n sum zNzN > > Silly me :| > > Tsjerk > > > On Mon, Jul 1, 2013 at 8:09 AM, Ankita naithani > > >wrote: > > > Hi Tsjerk, > > Thank you for y

[gmx-users] Re: Covariance file format

ted. But for > C-alpha only there is no difference between mass-weighted and > non-mass-weighted, except for global scaling. > > Cheers, > > Tsjerk > > > > On Mon, Jul 1, 2013 at 8:46 AM, Ankita naithani > > >wrote: > > > Hi Tsjerk, > > > &

Re: [gmx-users] continuing the terminated simulation

e posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ankita Naithani -- gmx-users mailing listgmx-users@gromac

[gmx-users] gmxcheck

d be quite helpful. Kind regards -- Ankita Naithani -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe reque

Re: [gmx-users] gmxcheck

:11 PM, Justin Lemkul wrote: > > > On 11/4/13 5:06 AM, Ankita Naithani wrote: > >> Hi, >> >> I was wondering if anyone could help me with the gmxcheck function? In the >> manual it is written, -m flag is given a LaTeX file will be written >> consisting of

Re: [gmx-users] gmxcheck

I do have the .mdp file. Main thing I was concerned about were details like number of water molecules added and number of counter ions added. Does gmxdump output that information? On Mon, Nov 4, 2013 at 12:19 PM, Justin Lemkul wrote: > > > On 11/4/13 7:14 AM, Ankita Naithani wrote

Re: [gmx-users] gmxcheck

Thanks Justin very much for your help. (Extremely silly and unthoughtful of me to forget this) Kind regards, Ankita On Mon, Nov 4, 2013 at 12:40 PM, Justin Lemkul wrote: > > > On 11/4/13 7:37 AM, Ankita Naithani wrote: > >> I do have the .mdp file. Main thing I was co