[gmx-users] Correlation-Covariance

the covariance matrix into correlation matrix or what is the relation between covariance and correlation matrix. I am not good in programming or mathematics, but if anyone could help me and give me some direction, I will be happy to write own program/script. Thanking you in advance, -- Dhananjay

[gmx-users] dynamic cross correlation map

-- Dhananjay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www

Re: [gmx-users] dynamic cross correlation map

Thanks you Tsjerk and all, Yes, the request was for residue correlations. Sorry for not mentioning it precisely. I will workout the solutions that were suggested here. But still, how can I get residue–residue-based correlated motions map ? Any other way or software ? -- Dhananjay On 9/18

[gmx-users] grompp error

--- Program grompp, VERSION 3.3.1 Source code file: topio.c, line: 388 Fatal error: Invalid order for directive moleculetype, file human_resistin_A43_mut_D43_A.itp, line 10 --- Confirmed (Star Trek) -- Dhananjay

[gmx-users] Error in pr

= 300.0 gen_seed= 173529 -- Dhananjay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un

[gmx-users] RMSD

for the RMSD calculations ? Or any other suggestion/programme please -- Dhananjay C Joshi Project Assistant LSB, C D F D ECIL Road, Nacharam Hyderabad-500 076, INDIA Tel : +91-40-27151344 Fax : +91-40-27155610 ___ gmx-users mailing listgmx-users

[gmx-users] mdrun error during pr

values! --- I was detained, I was restrained (The Smiths) Please anybody tell me what is wrong here ? for the reference I have attached pr.mdp file Thanking you in advance.. -- Dhananjay pr.mdp Description: Binary data

Re: [gmx-users] RMSD

residues Volume : 341.479 (nm^3) Density : 1005.02 (g/l) Number of SOL molecules: 10369 On 8/21/06, David van der Spoel [EMAIL PROTECTED] wrote: Dhananjay wrote: Hello all, I am running mdrun for a system of protein having 182 residues. (Before going for MD,mdrun for EM and PRhas been done

[gmx-users] pH

Hello all,Will it be possible to calculate pH of the system just before and after adding hydrogens ?If yes then how to calculate it ?Thanking you in advance.-- Dhananjay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman

[gmx-users] Join my Earthscreen network

I'm doing a little something for the earth, and I thought I'd invite you to join me: http://friends.earthscreen.com/?r=YQEUGBIHIyBVCWwNBCwLi=gmail[EMAIL PROTECTED]p=1z=1tc=15 ___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] tpr file

topology and all the simulation parameters... Do it mean that out of 3 *.tpr files (which are corresponding to above *.trr file that I joined) I can take any one ? Thanking you in advance. Dhananjay ___ gmx-users mailing listgmx-users

[gmx-users] topology database

in topology database of Gromacs? If yes then how to add it ? if anyone have any other solution please tell me -- Dhananjay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe