[gmx-users] Re: gmx-users Digest, Vol 59, Issue 138 (Doubt regarding membrane protein in POPC bilayer)

[Justin A. Lemkul]

When replying to digests, please change the subject line to something relevant.

Pawan Kumar wrote:
> Hello Justin Sir,
> 
> Greetings from Pawan.
> Sorry for the late reply.
> The max. force was 1.2447973e+o5 on atom 19448.

An Fmax that high is sure to generate problems.  It is up to you to inspect your 
system, understand which atoms are interacting to cause such a force, and 
determine if you've done something wrong.

-Justin

> This particular atom belongs to one of the lipid residues of the bilayer.
> I get Lincs warnings whenever I run the position restraint mdrun.
> 
> Thanking you,
> Pawan
> 
> 
> On Sat, Mar 21, 2009 at 6:08 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Pawan Kumar wrote:
> 
>         Hello Justin Sir,
> 
>         Greetings from Pawan
>         Thanks for your valuable suggestion and reply.
>         Initially I gave the emtol of 1000 and the output I got was :
>         Steepest Descents converged to machine precision in 163 steps
>         but did not reach the requested Fmax<1000.
>         Potential Energy = - 4.4516497e+05
> 
> 
>     ...and how close did Fmax get to 1000?
> 
> 
>         Even I tried to minimize the popc bilayer which I took from
>         Tieleman sir's website ( before generating a bigger bilayer
>         using genconf ) but that also converged to machine precision but
>         not to the requested Fmax<1000. How do I proceed further ?
> 
> 
>     Well, these things are not absolute; Fmax = 1000 is kind of a rule
>     of thumb that I use in my own work, but sometimes it is not
>     necessary.  Careful equilibration should massage your system into
>     cooperating.
> 
>     -Justin
> 
>         Thanks for your suggestions and help.
> 
>         Thanking you,
>         Pawan
> 
>         On Thu, Mar 19, 2009 at 9:13 PM,
> 
>            Pawan Kumar wrote:
>             > Hello Justin Sir,
>             >
>             > Greetings from Pawan
>             > Thanks for your valuable suggestion and reply.
>             > After inserting the protein in the bilayer using genbox I have
>            minimized
>             > the whole system without using any position restraints
>         (i.e. define =
>             > -DFLEXIBLE in em.mdp file). I used vanderwaal's distance
>         parameter (
>             > -vdwd of 0.6 ) in the genbox step.
>             > After running mdrun for energy minimization I got the
>         output as :
>             > Steepest Descents converged to Fmax<2250 in 14 steps.
>             > Potential energy = - 6.9484700e+05
>             > Maximum force = 2.2114819e+03 on atom 34277
>             > Norm. of force = 5.0103039e+04
>             >
> 
>            You should try for an Fmax of no greater than 1000.  2250 is
>         still
>            very high.
> 
>             > I tried decreasing the emtol value in the em.mdp file but it
>            ended with
>             > machine precision.
> 
>            How far did it converge?  What was Fmax?
> 
>             > I have read in literature that 5000 steps of Steetest
>         Descents run is
>             > required after inserting the protein in the bilayer which
>         should be
>             > followed by atleast 1000 steps of conjugate gradients. How
>         can I
>             > accomplish this ? Is there any parameter to be given in the
>            em.mdp file
>             > ? I use steep as the integrator in the mdp file for energy
>            minimization.
> 
>            Read the manual.
> 
>            Whether or not that exact setup is going to be "required" is
>         likely
>            system-specific.  I would say that as long as your system
>         converges
>            to a stable,
>            negative Epot with a reasonable Fmax (less than 1000, but ideally
>            lower) then
>            you *may* have an appropriate starting structure.
> 
>            -Justin
> 
>             > Please help with some suggestions.
>             > Thanks in advance.
>             >
>             > Thanking you,
>             > Pawan
>             >
>             >
>             >
> 
> 
> 
>         ------------------------------------------------------------------------
> 
>         _______________________________________________
>         gmx-users mailing list    gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>         http://www.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 gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>.
>         Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     ICTAS Doctoral Scholar
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
>     _______________________________________________
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://www.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 gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================