[gmx-users] g_rmsf Analysis.

e same fitting. Let me know if I am doing a mistake. Thanks. Vivek Modi Graduate Student, IITK. -- 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 p

[gmx-users] Re: Reference structure for PCA.

have few questions related to your query: > >> > >> During covariance matrix calculation, g_covar by default takes average > >> structure of the trajectory as a reference structure then why you are > >> giving it average structure of your trajectory (0-100ns

[gmx-users] Re: gmx-users Digest, Vol 106, Issue 52

appropriate and why ? Thanks and Regards, -Vivek. On Thu, Feb 7, 2013 at 1:26 PM, vivek modi wrote: > > > Hello, > > > > I have troubled you with a similar question before also, but I guess I > need > > some more clarification. My question is about the refere

[gmx-users] Re: Reference structure for PCA.

Any comments/help on this query. I am stuck with this. Thanks, -Vivek. On Thu, Feb 7, 2013 at 1:26 PM, vivek modi wrote: > Hello, > > I have troubled you with a similar question before also, but I guess I > need some more clarification. My question is about the reference struct

[gmx-users] Re:Re: PCA on secondary structure of protein.

; > > Content-Type: text/plain; charset=ISO-8859-1 > > Sure! > > You'll just be looking at correlations between secondary structure > elements, disregarding the role that the loops may play. But it's a > sound approach. > > :) > > Tsjerk > &g

[gmx-users] PCA on secondary structure of protein.

which do not play any role. Is it appropriate to group only the helices together ignoring the loops and perform PCA ? Any help is appreciated. Regards, -Vivek Modi Graduate Student IITK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] Re: Re: Re: Reference structure for g_covar

#x27;re sort of still on the road from A (the starting > position) to B (the equilibrated state). > > Hope it helps, > > Tsjerk > > On Oct 20, 2011 5:07 PM, "vivek modi" wrote: > > Hi Tsjerk, > > Thanks a lot for your reply. > But now I will ask a very naive

[gmx-users] Re: Re: Reference structure for g_covar

? Thanks a lot. Regards, -Vivek Modi Date: Wed, 19 Oct 2011 13:58:00 +0200 > From: Tsjerk Wassenaar > Subject: Re: [gmx-users] Reference structure for g_covar > To: Discussion list for GROMACS users > Message-ID: > > > Content-Type: text/plain; charset=ISO-8859-

[gmx-users] Reference structure for g_covar

? Any help is appreciated. Thanks a lot. Regards, Vivek Modi Graduate Student, IITK. -- 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

[gmx-users] Re: gmx-users Digest, Vol 72, Issue 21

st..." > > > Today's Topics: > > 1. dssp FATAL ERROR. (vivek modi) > 2. Re: dssp FATAL ERROR. (Justin A. Lemkul) > 3. Restraints of COM (Eudes Fileti) > 4. Restraints of COM 2 (Eudes Fileti) > 5. T

[gmx-users] dssp FATAL ERROR.

p it gives the following error: Program do_dssp_4, VERSION 4.0.5 Source code file: do_dssp.c, line: 471 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddXnSQTc ddgMjECf > /dev/null 2> /dev/null Any help is appreciated. Thanks. Vivek Modi, Graduate Student, IITK. --

[gmx-users] No default Proper Dih. types

hi, I am simulating a protein complex. The peptide in the complex has PRO at the N-terminal. I run pdb2gmx and choose PRO-NH as the cap for the respective N-terminal. pdb2gmx_4mpi -f xyz.pdb -o -ter -ignh -o conf.gro Select N-terminus type (start) 0: PRO-NH2+ 1: PRO-NH 2: NH3+ 3: None 1 N-t