[gmx-users] Re: gmx-users Digest, Vol 63, Issue 148

[Thomas Schlesier]

> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 29 Jul 2009 16:04:54 -0700 (PDT)
> From: "Johnny Lam" <johntus at berkeley.edu>
> Subject: [gmx-users] Pulling a CG protein
> To: gmx-users at gromacs.org
> Message-ID:
>         <55658.128.32.142.63.1248908694.squirrel at calmail.berkeley.edu>
> 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: johntus at berkeley.edu
>