[gmx-users] gmxcheck

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 requests to the list

Re: [gmx-users] gmxcheck

:11 PM, Justin Lemkul jalem...@vt.edu 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 a rough outline for a methods section

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 jalem...@vt.edu wrote: On 11/4/13 7:14 AM, Ankita Naithani

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 jalem...@vt.edu wrote: On 11/4/13 7:37 AM, Ankita Naithani wrote: I do have the .mdp file. Main thing I was concerned about

Re: [gmx-users] continuing the terminated simulation

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/mailman/listinfo/gmx-users * Please search the archive at http

[gmx-users] Re: Covariance file format

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 at 1:38 AM, Ankita naithani ankitanaith...@gmail.comjavascript

[gmx-users] Re: Covariance file format

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 ankitanaith...@gmail.comjavascript:; wrote: Hi Tsjerk, Thank you for your reply. So, these are the eigenvectors. By any chance, can we obtain

[gmx-users] Re: Covariance file format

-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 ankitanaith...@gmail.comjavascript:; wrote: Hi Tsjerk, Coffee is always magical, I tell you. Just a sniff

Re: [gmx-users] Eigenvector and eigenvalues

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 On Sat, Jun 8, 2013 at 1:06 PM, Ankita naithani ankitanaith...@gmail.com wrote: Hi

Fwd: [gmx-users] Eigenvector and eigenvalues

wrote: 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 ankitanaith...@gmail.com wrote: Hi, I wanted to know about the eigenvectors and eigenvalues. I recently performed

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 jalem...@vt.edu wrote: On 6/5/13 3:03 PM, Ankita naithani wrote: Hi, I have two questions. I have performed a simulation on my protein structure and after

[gmx-users] Eigenvector and eigenvalues

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 the archive

[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] rmsf analysis

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/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] Re: rmsf analysis

)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/mailman/listinfo/gmx-users

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

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@gromacs.org http://lists.gromacs.org

[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 ankitanaith...@gmail.com

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

at 5:28 PM, Justin Lemkul jalem...@vt.edu 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 checkpoint file of version 13 with code of version 12 Can anyone please help

Re: [gmx-users] TIP4P water model

as the [molecules] section of the topology, to at least start to guess at what's wrong. It is unusual to find a failure in grompp before genion. -Justin On 2012-09-21 04:48:37PM +0100, Ankita naithani wrote: Hi all, I am trying to begin a simulation of a protein. I am using AMBER99sb-ILDN

[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

for the difference? On Sun, Sep 16, 2012 at 3:03 PM, Mark Abraham mark.abra...@anu.edu.au 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 a difference of 10 atoms

[gmx-users] Topology file

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.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive

[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 ankitanaith...@gmail.com wrote: Hi, I noticed that in my topology file, there is no inclusion of position restraint file for my

[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)subscribe

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 mark.abra...@anu.edu.au 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 co-ordinate

[gmx-users] Protein-ligand - genion error

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-users

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 jalem...@vt.edu wrote: On 8/10/12 1:05 PM, Ankita naithani wrote: Dear All, I

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 jalem...@vt.edu wrote: On 8/10/12 1:26 PM, Ankita naithani wrote: Hi Justin, Thank you

[gmx-users] Protein - Ligand tetramer simulation

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.gromacs.org

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 jalem...@vt.edu wrote: On 8/9/12 10:40 AM, Ankita naithani wrote: Hi all, I am trying