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[gmx-users] query about generation of 2D histogram

Respected Sir,     I am trying to generate free energy landscape by using g_sham,From the archive I came to know that one .xvg file needs to be prepared containing three columns of data, first one is time, 2nd and 3rd one are the coordinates of interest, I used the command g_sham -f *.xvg

[gmx-users] query about free energy landscape

Dear Sir,     I am facing one problem regarding generation of Free energy landscape (FEL); I have some doubt regarding the algorithm of g_sham. I will be highly obliged if you kindly let me clear my doubt. I know that three variables are needed for construction of 3D energy landscape.

[gmx-users] query about simulation of a protein containg a metal ion

pdb2gmx CA2+ ion is considered as follows. type    resnr residue CA2+  CA    CA Please suggest what should be taken into account while running the simulation with the metal ion. regards Sangeeta Kundu See the Web#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz

[gmx-users] query regarding coming out of ligand from protein during simulation

Dear all,           I am trying to perform simulation of a protein with several ligands, in case of certain ligands I found that the ligand  is coming out of the protein after 5-6 ns. I have checked the energy of the system, but it does not show any abrupt change, still the ligand is coming out

[gmx-users] query about random velocity generation

Dear Sir,   I want to simulate the same system at different temperatures using different velocities want to investigate whether the simulations converged or not.. For that should we alter the default  gen_seed value, if yes, then can  we choose the gen_seed value arbitrary or  is there any

[gmx-users] query about essential dynamics

Dear all,       I performed essential dynamics analysis on two proteins at different temperatures ranging from 300 K to 473 K; subsequently I tried to calculate RMSIP (root mean square inner product) to determine the subspace overlap between two different trajectories at different

[gmx-users] problem regarding energy minimization

Dear Sir, I want to minimize an average structure obtained from a simulation, by conjugate gradient method.. As this method is more efficient than steepest descent I am trying with this method. The minimization has gone smoothly with steepest descent and lbfgs, but it failed while using

[gmx-users]query regarding unfolding of protein at higher temperature

Dear Sir, I have found in literature that most of the unfolding studies of proteins are performed at higher temperature by increasing box size accordingly. My protein has approximately 70 residues, I want to simulate it at room temperature as well as at some higher temperatures. I have not

[gmx-users] problem regarding mdrun and g_hbond

Dear all, I gave a simulation run of a protein using G43a1force field at 523K using Berendson's Temperature coupling for 10 ns, But three times it failed with the messege segmentation fault , without giving any other error messege. Previously I ran the simualtion of the same protein

Re: [gmx-users] problem regarding mdrun and g_hbond

? Tsjerk On 3/15/07, Erik Marklund [EMAIL PROTECTED] wrote: 15 mar 2007 kl. 08.29 skrev sangeeta kundu: Dear all, I gave a simulation run of a protein using G43a1force field at 523K using Berendson's Temperature coupling for 10 ns, But three times it failed with the messege

Re: [gmx-users] problem regarding mdrun and g_hbond

that, you may be better off adding some additional sodium chloride... One sodium may balance the net charge, but it will not balance a charged protein. Cheers, Tsjerk On 3/15/07, sangeeta kundu wrote: Dear All, Thanks a lot to Mark,Tsjerk and Erik your promt reply. It is a globular protein

[gmx-users] query about .xpm file

into a postscript file, so that every residue and the time scale will be clearly visible, PLease help. regards Sangeeta Kundu Research Fellow Bioinformatics Centre Bose Institute Kolkata India __ Yahoo! India Answers: Share what

Re: [gmx-users] query about .xpm file

] query about .xpm file Date: Thu, 22 Feb 2007 11:28:16 +0100 sangeeta kundu wrote: Dear Sir, I converted the output of do_dssp program (.xpm file) into an .eps file by the command xpm2ps,I also specified the size by -size command, but the problem is that when I am observing

Re: [gmx-users] query about .xpm file

Dear Sir, Sorry, just now I have seen that -skip is mentioned in xpm2ps not in do_dssp, So I ran it with Do_dssp. I apologize for that . regards Sangeeta __ Yahoo! India Answers: Share what you know. Learn something new

Re: [gmx-users] query about .xpm file

Dear Sir, I can change the output with -bx and -by , but problem is the tick marks become quite illegible.and I does not display the number of residue etc. regards Sangeeta --- David van der Spoel [EMAIL PROTECTED] wrote: sangeeta kundu wrote: Dear Sir, I converted the output

Re: [gmx-users] query about .xpm file

of -bx and -by , the Secondary str file improves, but no improvement in the time scale, rather each time a black bar is displayed. How can I get the appropriate time scale? regards SANGEETA --- David van der Spoel [EMAIL PROTECTED] wrote: sangeeta kundu wrote: Dear Sir, I converted

RE: [gmx-users] query about g_rdf and make_ndx

Thanks a lot to Dr Sica and Dr. Warren. regards Sangeeta - Here’s a new way to find what you're looking for - Yahoo! Answers ___ gmx-users mailing list

[gmx-users] query about g_rdf and make_ndx

Dear All, I want to calculate the rdf of a particular residue with respect to water, I was able to generate the rdf of the entire protein against the bulk water,but I could not do the same for a particular residue, In the index.ndx file I have specified the groups of that

[gmx-users] How to generate plot of tertiary contact over time

Can anyone suggest me how to generate a plot which shows the variation of tertiary contact over time. regards Sangeeta - Here’s a new way to find what you're looking for - Yahoo! Answers

Re: [gmx-users] How to generate plot of tertiary contact over time

dear Sir, Thanks for suggestion. regards SANGEETA --- Mark Abraham [EMAIL PROTECTED] wrote: sangeeta kundu wrote: *Can anyone suggest me how to generate a plot which shows the variation of tertiary contact over time.* Curiously enough, a careful look at section 7.4

RE: [gmx-users] problem still lies regarding dssp

: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of sangeeta kundu Sent: Mon 12/02/2007 9:55 AM To: Discussion list for GROMACS users Subject: RE: [gmx-users] problem still lies regarding dssp Dear Abu and Mark, You asked me

[gmx-users] problem still lies regarding dssp

Dear All, I do not know whether I am interrupting you again and again by asking the same question, but I am helpless , I can not detect my fault, When I run the program DSSP it works fine, but while executing do_dssp or my_dssp (as suggested by Yang) the program seems to be

[gmx-users] why protein comes out of the box

Dear Sir, I am facing one problem, I gave the MD run of a protein of approximately 70 residues for 10ns, after 1 ns run part of protein was getting out of the waterbox and at the end of 10 ns I found that almost half of the protein was coming out of the waterbox, I gave the

Re: [gmx-users] why protein comes out of the box

THANKS A LOT TO ERIK AND MARK regards SANGEETA Mark Abraham [EMAIL PROTECTED] wrote: sangeeta kundu wrote: *Dear Sir,* ** * I am facing one problem, I gave the MD run of a protein of approximately 70 residues for 10ns, after 1 ns run part of protein was getting out