Re: [gmx-users] confirm bdd22a55a5075c60cd9dc4382a75e0b7689a1d11

2008-04-19 Thread Mark Abraham
munuswamy baskar wrote: Sir/Mam, please tell me what program in Gromacs have I to use to know how many water molecules reacting on the surface of the solute molecule in the cubic box about 3.0A unit distance from the surface of the solute. I don't understand what you are trying to do, but i

Re: [gmx-users] Error of mdrun

2008-04-19 Thread Mark Abraham
s lal badshah wrote: Dear Experts, Hi ! I am doing MD simulation on two computer, on one when I want to start the EM and do the mdrun command the following error results: linux:~/project # mdrun -v -s em.tpr -c em.pdb mdadm: /dev/md-v not identified in config file. linux:~/project # mdrun -v

[gmx-users] Discussion, weixin wants to chat

2008-04-19 Thread weixin
I've been using Google Talk and thought you might like to try it out. We can use it to call each other for free over the internet. Here's an invitation to download Google Talk. Give it a try! --- weixin wants to stay in better to

[gmx-users] Error of mdrun

2008-04-19 Thread s lal badshah
Dear Mark, When I enter from root account the following is the result: linux:~ # which mdrun /sbin/mdrun linux:~ # which grompp /usr/bin/grompp linux:~ # But from user account the which mdrun usr/bin/mdrun and also the which grompp /usr/bin/grompp occured. Actually I have very little experi

Re: [gmx-users] Error of mdrun

2008-04-19 Thread Mark Abraham
s lal badshah wrote: Dear Mark, When I enter from root account the following is the result: linux:~ # which mdrun /sbin/mdrun linux:~ # which grompp /usr/bin/grompp linux:~ # But from user account the which mdrun usr/bin/mdrun and also the which grompp /usr/bin/grompp occured. Actually I hav

[gmx-users] Free energy calculation

2008-04-19 Thread shuai lu
Hello everyone, Here i want to caculate the binding free energy between an ligand and its receptor. Should I set free_energy as "yes" in Free Energy Perturbation Part or use g_lie by doing recepto-ligand-solvate md and ligand-solvate md separately? If run a md by set free_energy as "yes", how s

Re: [gmx-users] Free energy calculation

2008-04-19 Thread Justin A. Lemkul
Quoting shuai lu <[EMAIL PROTECTED]>: > Hello everyone, > > Here i want to caculate the binding free energy between an ligand and its > receptor. Should I set free_energy as "yes" in Free Energy Perturbation Part Yes, among other things. Read the manual regarding all the free energy options. Si

Re: [gmx-users] water can't freeze

2008-04-19 Thread Sagittarius
Send me please your files, I would like to have a look at them   Alex--- On Fri, 4/18/08, Wei, Xiupeng <[EMAIL PROTECTED]> wrote: From: Wei, Xiupeng <[EMAIL PROTECTED]>Subject: [gmx-users] water can't freezeTo: "gmx-users@gromacs.org" Date: Friday, April 18, 2008, 8:41 PMHi gmx users, I'm

Re: [gmx-users] water can't freeze

2008-04-19 Thread Vasilii Artyukhov
Dear Xiupeng, What you're seeing is the difference between freezing water and overcooling it. If you want your water to crystallize, you'll actually have to make it - e.g., by putting it in contact with ice. Normally, pure water doesn't freeze on its own, you can easily verify this experimentally

Re: Re: [gmx-users] Free energy calculation

2008-04-19 Thread shuai lu
Dear Justin, Thank you very much for helping me again! Best wishes! 2008/4/20, [EMAIL PROTECTED] <[EMAIL PROTECTED]>: > > Send gmx-users mailing list submissions to >gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit >http://www.gromacs.org/mailma

[gmx-users] a question

2008-04-19 Thread shahrbanoo karbalaee
dear sir/madam I am doing MD ap peptide with gromacs.this peptide( 13 residue) has a NH2 in c terminal.I change it from heteroatom to atom but it take a error.and it say :I acnnot find C alpha for residue 14 NH2 WHILE COMBINING tdb and rtp.what do i do ? best -- sh-karbalaee __

Re: [gmx-users] a question

2008-04-19 Thread Mark Abraham
shahrbanoo karbalaee wrote: dear sir/madam I am doing MD ap peptide with gromacs.this peptide( 13 residue) has a NH2 in c terminal.I change it from heteroatom to atom but it take a error.and it say :I acnnot find C alpha for residue 14 NH2 WHILE COMBINING tdb and rtp.what do i do ? This is

Re: [gmx-users] a question

2008-04-19 Thread David van der Spoel
shahrbanoo karbalaee wrote: dear sir/madam I am doing MD ap peptide with gromacs.this peptide( 13 residue) has a NH2 in c terminal.I change it from heteroatom to atom but it take a error.and it say :I acnnot find C alpha for residue 14 NH2 WHILE COMBINING tdb and rtp.what do i do ? -ter b