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

Kirill Bessonov kbessonov at gmail.com
Thu Jul 16 21:08:52 CEST 2009

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?
-How I can improve on EM, what kinda setting in mdp file can I use to that
system converges even after 10,000 steps?
-How to prevent clashes, maybe there are some settings to try with genbox
-cp -cs command?

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