[gmx-users] Peptide - DMPC membrane simulations -> Unstable system

[Justin A. Lemkul]

Kirill Bessonov wrote:
> Hi guys,
> 
> I am trying to start simulation on lipid - peptide system, but receive 
> LINCS warnings of angles rotating more than 30 deg which means that my 
> system is unstable. I have tried to do mdrun on the DMPC box itself and 
> had no problems. Once I insert my peptide, the problems starts. I have 
> run Energy MInimization with LIncs order or 4 and Lincs iterations 8, 
> but still could not bring system to 200 kJ/mol Fmax.  Received the 
> following message.
> 
> Converged to machine precision,
> but not to the requested precision Fmax < 100
> 
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
> 
> writing lowest energy coordinates.
> 
> Back Off! I just backed up sys_EM_ready.gro to ./#sys_EM_ready.gro.2#
> 
> Steepest Descents converged to machine precision in 499 steps,
> but did not reach the requested Fmax < 100.
> Potential Energy  = -1.2830664e+06
> Maximum force     =  3.4162991e+03 on atom 2
> Norm of force     =  3.2566280e+01
> 
> Now I am trying to just to do EM (energ. minim) on my 14 aa peptide, in 
> water box just to see if it will work.
> 
> My questions:
> -How to position peptide into existing lipid box (apart form using 
> editconf -rotate parameter). I have tried VMD and did it visually, but 
> new coordingates were not saved?

I wrote a tutorial that gives instructions on how to build membrane protein 
systems, you might find it useful:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html

> -How I can improve on EM, what kinda setting in mdp file can I use to 
> that system converges even after 10,000 steps?

emstep and emtol are the relevant parameters.  Setting nsteps is the maximum 
amount of steps allowed; I don't think there is a way (or a reason) to force EM 
to run to 10,000 steps.

> -How to prevent clashes, maybe there are some settings to try with 
> genbox -cp -cs command?
> 

You could use genbox, but often what happens is there are substantial voids 
between the peptide and lipids.  Water seeps in and you have to equilibrate for 
a lot longer.  See my tutorial above for more rigorous building methods.

-Justin

> Thanks
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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

Justin A. Lemkul
Ph.D. Candidate
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

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