Hi Johnny, i replied something to the pull-code of your question. But problem was, i didn't edited the subject line... So here is my answer (see below) with the right subject line (so that you hopefully find it). Hope it helps you. Thomas
> > Message: 3 > Date: Thu, 30 Jul 2009 12:08:40 -0700 (PDT) > From: "Johnny Lam" <[email protected]> > Subject: Re: [gmx-users] Pulling a CG protein > To: [email protected] > Cc: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain;charset=iso-8859-1 > > Hi XAvier, Marc, and David, > > Thank you so much for the reply and encouragement ;-). Please forgive me > as I am trying to learn how to reply to the thread that I started. With > regards to the fun discussion, it was my original intent to compare the > results of pulling with the MARTINI forcefield (if the pull code was > correct) with already published works on MD (using all-atomistic modeling > of course :-)). I just wanted to know whether the pull code that I am > using will be valid at all. If you guys can verify that would be awesome! > Otherwise, I'd be happy to share the results with you guys if you wish. > Again, thanks! > > --Johnny > > > ------------------------------------------------- > Johnny Lam > ISPE Berkeley Chapter External Vice President > Department of Bioengineering > College of Engineering > University of California, Berkeley > Tel: (408) 655- 6829 > Email: [email protected] > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Wed, 29 Jul 2009 16:04:54 -0700 (PDT) > > From: "Johnny Lam" <[email protected]> > > Subject: [gmx-users] Pulling a CG protein > > To: [email protected] > > Message-ID: > > <[email protected]> > > Content-Type: text/plain;charset=iso-8859-1 > > > > Dear gromacs users, > > > > Hi, I am trying to pull apart a relatively large protein (CG using the > > martini force field) by pulling on two groups in opposite directions. To > > do this, I will be using the following .mdp file. However, I am almost > > certain that it contains errors: > > -snip > > > > ; Pulling > > pull = afm > > pull_geometry = direction > > pull_start = no > > pull_nstxout = 10 > > pull_nstfout = 10 > > pull_ngroups = 2 > > pull_group0 = > > pull_group1 = pull > > pull_vec1 = -0.1764 -0.9823 -0.0625 > > pull_init1 = -0.1764 -0.9823 -0.0625 > > pull_rate1 = 0.0001 > > pull_k1 = 1000 > > pull_group2 = freeze > > pull_vec2 = 0.1764 0.9823 0.0625 > > pull_init2 = 0.1764 0.9823 0.0625 > > pull_rate2 = 0.0000000001 > > pull_k2 = 5000 > > > > Think the first problem is the: pull = afm In the manual there is no more a 'afm' option, but as far as i know 'umbrella' should be the same (don't ask me why there was no error message about this). If you have no pull_group0 you could get problem with the com-motion. If you want to pull 'pull' away from 'freeze', i would do the following: pull = umbrella pull_geometry = position pull_start = yes (we don't want to calculate the initial distance between 'pull' and 'freeze' by hand) pull_ngroups = 1 (because the reference group doesn't count to this value) pull_dim = Y Y Y (because we want to pull in 3D) pull_group0 = freeze pull_group1 = pull pull_vec1 = vector from 'freeze' to 'pull' pull_init1 = 0.0 0.0 0.0 Now you are pulling 'pull' away from 'freeze' and and you should have no problem with com-motion. If you want to fix the position of 'freeze' i would use position_restraints. One thing: once i had problems with the 'pull_weightsX', i got (with one system) every time error messages (i had only 1atom in each group and tried the values 0 and 1 both, but didn't work). So i left these to values blank and GROMACS selected them, and it worked. In other simulations with a similar setup i had no problems with 'pull_weightsX'. > > The reason why group 2 has such a high force constant and low pull rate is > > because I wanted to simulate putting a harmonic constraint on the freeze > > group. However, when I process this .mdp with grompp, I get the following > > message: > > > > WARNING 1 [file md_vinculin.mdp, line unknown]: > > Unknown or double left-hand 'pull_group2' in parameter file Another thing could be that you have no index group with the name 'freeze'? But best have also a look in the new (GROMACS 4) manual. COM pulling is described from page 156 on. Hope this helps Thomas > > > > > > > > WARNING 2 [file md_vinculin.mdp, line unknown]: > > Unknown or double left-hand 'pull_vec2' in parameter file > > > > > > The version of gromacs I have running on my powerpc is 4.0.5 so the pull > > code should be implemented in the .mdp file. I am not sure if I specified > > the parameters correctly. Please help! Thanks! > > > > --Johnny > > > > ------------------------------------------------- > > Johnny Lam > > ISPE Berkeley Chapter External Vice President > > Department of Bioengineering > > College of Engineering > > University of California, Berkeley > > Tel: (408) 655- 6829 > > Email: [email protected] > > _______________________________________________ gmx-users mailing list [email protected] http://lists.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 interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
