Re: [gmx-users] Problem in downloading source code

Dear Mark, Thanks for your reply. But still I am unable to download , and with same error reported in the downloading page as mentioned in my previous mail. Others membering from different locations reading this mail could please test the link and report here would be useful for me. The browser th

Re: Re: [gmx-users] Position restricted md

 yes , I had gone through the manual, but is that all? I mean to say that even if the protein suffers from high solvent forces (though the energy minimisation can be done over the whole system ie protein in solvated state) that may not pose much of a problem , in case we simulate for suffici

Re: [gmx-users] Problem in downloading source code

Hi, On Tuesday, 23. October 2007 09:24, raja wrote: > Dear Mark, > > Thanks for your reply. But still I am unable to download , and with same > error reported in the downloading page as mentioned in my previous mail. > Others membering from different locations reading this mail could please > tes

Re: [gmx-users] Position restricted md

sarbani chattopadhyay wrote: yes , I had gone through the manual, but is that all? I mean to say that even if the protein suffers from high solvent forces (though the energy minimisation can be done over the whole system ie protein in solvated state) that may not pose much of a problem , in c

Re: Re: [gmx-users] Position restricted md

 I understand.Thank you for the comparative analysis. sarbani On Tue, 23 Oct 2007 Mark Abraham wrote : >sarbani chattopadhyay wrote: >> yes , I had gone through the manual, but is that all? I mean to say that >

RE: [gmx-users] frequence from PCA eigenvalue

From: [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] frequence from PCA eigenvalue Date: Mon, 22 Oct 2007 20:37:10 +0200 (MEST) Dear community, I have done a principal component analysis on an MD trajectory (g_covar) and would l

Re: [gmx-users] Problem in downloading source code

Hi Florian, Thanks for your reply. I tried to ftp through wget...but still not workingI pasted the output of wget hereunder. # D:\Biosoftwares\wget>wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.2.tar.gz --14:11:41--

[gmx-users] alpha Carbon-Aromatic ring hydrogen bond

 Hi, I want to analyze the Hydrogen bond between alpha Hydrogen and aromatic ring over the simulation time.g_hbond can't recognise this bond.is there any command by which i can do that?

[gmx-users] problem in g_confrms

Dear sir, I am trying to fit two confomations of a protein using g_confrms command. The program is giving the result but when I am trying to use two different proteins it is giving the following error. command: g_confrms -f1 1prg.pdb -f2 speptide.pdb -o fit.pdb --- Then it asked to "Selec

Re: [gmx-users] Position restricted md

Doing position-restrained simulation is useful to equilibrate solvent and ions. If you would like to study the dynamics of the peptide, PRMD doesn't help. PRMD is usually performed before production run for a duration from several hundred ps to 1ns. Regards, Yang Ye - Original Message

[gmx-users] entropy calaculted script??

Dear Gro-usr friends: I want to calculat the entropy during the md,but lack calculting script for the entropy. Who can provide it for me? Thank you very much! - @yahoo.cn 新域名、无限量，快来抢注！___ gmx-users mailing lis

Re: [gmx-users] entropy calaculted script??

I doubt that no one could give you such script. To plot free energy surface, you can utilize Rg/Q or Rg/ContactNumber or dPCA (http://wiki.gromacs.org/index.php/Dihedral_PCA) analysis. Regards, Yang Ye - Original Message From: xi zhao <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Se

[gmx-users] g_rmsf and pbc

Dear all, The protein I am working on is rubisco, consisting of 8 identical large subunits and 8 identical small subunits. I try to calculate RMSF for each large subunits, but the rmsf values seems much large to some large subunits. So I check the first frame of the protein structutre, and I fo

Re: [gmx-users] g_rmsf and pbc

tangxuan wrote: Dear all, The protein I am working on is rubisco, consisting of 8 identical large subunits and 8 identical small subunits. I try to calculate RMSF for each large subunits, but the rmsf values seems much large to some large subunits. So I check the first frame of the protein st

Re: [gmx-users] alpha Carbon-Aromatic ring hydrogen bond

sarbani chattopadhyay wrote: Hi, I want to analyze the Hydrogen bond between alpha Hydrogen and aromatic ring over the simulation time.g_hbond can't recognise this bond.is there any command by which i can do that? Try g_dist -h Mark ___ gmx-

Re: [gmx-users] problem in g_confrms

harpreet singh wrote: Dear sir, I am trying to fit two confomations of a protein using g_confrms command. The program is giving the result but when I am trying to use two different proteins it is giving the following error. command: g_confrms -f1 1prg.pdb -f2 speptide.pdb -o fit.pdb --

Re: [gmx-users] g_rmsf and pbc

Mark,thanks for your reply. I am not sure what happened and I can show you the error message," Group 101 ( chK_chM) has 4070 elements Group 102 ( chM_chO) has 4070 elements Group 103 ( chO_chI) has 4070 elements Group 104 ( chJ_chL) has 4070 elements Group 105 ( c

Re: [gmx-users] g_rmsf and pbc

tangxuan wrote: Mark,thanks for your reply. I am not sure what happened and I can show you the error message," Group 101 ( chK_chM) has 4070 elements Group 102 ( chM_chO) has 4070 elements Group 103 ( chO_chI) has 4070 elements Group 104 ( chJ_chL) has 4070 elements G

Re: [gmx-users] entropy calaculted script??

xi zhao wrote: Dear Gro-usr friends: I want to calculat the entropy during the md,but lack calculting script for the entropy. Who can provide it for me? Thank you very much! g_anaeig in the cvs head version does it, but it is not too difficult to do it yourself based on the eigenvalues. read th

[gmx-users] missing Ryckaert-Bell in 3.3.2 is now considered as ERROR?

Hi all, has the default behaviour of 3.3.1 -> 3.3.2 changed from Warning to Errors concerning this?: AFAIR in 3.3.1 WARNING ... No default Ryckaert-Bell. types, using zeroes to: ERROR 1 [file "topol.top", line 159]: No default Ryckaert-Bell. types in 3.3.2 Best Martin ___

[gmx-users] Source code through email

Dear listmembers, I am already running gromacs earlier version, now when I try to upgrade to newer version, I could not download latest source code from the gromacs website. If anyone have the latest gromacs release gromacs-3.3.2.tar.gz with them, please send it to me through email. With thanks,

Re: [gmx-users] Source code through email

raja wrote: Dear listmembers, I am already running gromacs earlier version, now when I try to upgrade to newer version, I could not download latest source code from the gromacs website. If anyone have the latest gromacs release gromacs-3.3.2.tar.gz with them, please send it to me through email.

[gmx-users] make_ndx

 hi, I want to select two groups in the index file, one group consisting of only the aromatic ring of phenylalanine and the other group consisting of only the alpha carbon. I want to know the way to use the make_ndx command for this. ___ gmx-use

Re: [gmx-users] make_ndx

sarbani chattopadhyay wrote: hi, I want to select two groups in the index file, one group consisting of only the aromatic ring of phenylalanine and the other group consisting of only the alpha carbon. I want to know the way to use the make_ndx command for this. After entering make_ndx

Re: Re: [gmx-users] make_ndx

 Thanks Mark, I could do it following your suggestion. Sarbani On Wed, 24 Oct 2007 Mark Abraham wrote : >sarbani chattopadhyay wrote: >> hi, >> I want to select two groups in the index