[gmx-users] Problem with equilibrated lipid bilayer structure

Thomas Piggot t.piggot at soton.ac.uk
Mon Oct 15 11:40:16 CEST 2012

Hi Jernej,

The CHARMM force field was developed for use with the TIP3P model making 
this probably the appropriate choice, even if this model may not perform 
the best for simulations of pure water (see 
http://pubs.acs.org/doi/abs/10.1021/jz200167q for some more details).

As for some specific GROMACS points with the CHARMM36 lipids. Firstly I 
recommend you to use the CHARMM TIP3P variant and secondly you should 
also be careful with the cut-off's you choose. I do not think a 
dispersion correction would be appropriate and you should also probably 
be using some different cut-off's to those you give in you mdp 
(typically a switching off of the van der Waals interactions is done 
with this force field). Finally you also need to be careful constraining 
all bonds (instead of just bonds to hydrogen atoms) with this force 
field. We found that we needed to increase the accuracy of the LINCS 
settings when constraining all bonds to ensure energy conservation.



Peter C. Lai wrote:
> On 2012-10-15 03:10:18PM +0800, Jernej Zidar wrote:
>> The reason for using SPCE instead of TIP3P is that it performs  way
>> better than TIP3P. This point is being emphasized everywhere along the
>> documentation. I will try simulating using TIP3P model.
>>> Is there a reason to switch water models? Gromacs supports both the
>>> traditional TIP3P and the CHARMM TIP3P (TIPS3P).
>>> Since you need to reinitialize velocities, it may not be a good idea to use
>>> Nose-Hoover and Parinello-Rahman straight away. Furthermore, you need
>>> to gen_vel=yes since gromacs has no velocity from your previous charmm run
>>> and subjecting an otherwise frozen system to a parinello-rahman thermostat is
>>> asking for trouble.
>> gen_vel=yes does not seem to help
> Have you tried just doing NVT with tcoupl = V-rescale and tau_t = 0.1 0.1?
>>> Also, pressure coupling for NPT should probably be semiisotropic for bilayers.
>>> Finally you may want to experiment with EnerPres; see also
>>> http://pubs.acs.org/doi/abs/10.1021/ct3003157 (although this isn't related to
>>> your crash).
>> EnerPres is already set.
>>   I tried your suggestions but the simulation still fails.
>> Best,
>> Jernej Zidar
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Dr Thomas Piggot
University of Southampton, UK.

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