From: Nicholas Musolino (musolino_at_mit.edu)
Date: Sun Oct 17 2010 - 10:27:40 CDT
On Oct 17, 2010, at 11:18 AM, mjyang wrote:
> Dear Nicholas,
> Thanks for your reply.
> I gradually heated the system from 100K to 600K by an increment of 50K (100, 150, 200, 250, ..., 600K). For each segment, 50,000 MD steps was carried out under NPT ensemble and 2fs time step.
> We performed the high-temperature MD simulation to produce a set of distinct conformations for a small protein. From each conformation, a long MD simulation will be carried out to study its folding.
>
> The following three NPT schemes were tested and the expansion occured in all cases:
> scheme a: temperature control 1 and pressure control 1
> scheme b: temperature control 1 and pressure control 2
> scheme c: temperature control 2 and pressure control 2
>
> I am not sure whether the expansion always occured at high temperature simulation under NPT ensemble.
> Could someone please tell me how to fix this problem?
Hello Mingjun,
I think the purpose you described (explore conformational space more quickly than sampling at 20 C) makes sense.
To fix this problem, you will need to think further about the choice of pressure and temperature targets. What is the expected behavior of an aqueous system at 600 K and 1.0 atm? What can these values be, given the purposes of the simulation?
Another note: is a 2 fs timestep okay for your system? Have you tested this in a microcanonical sim. to see if the integration is conservative/accurate? This is not related to your expansion problem, just another small issue I saw.
Hope this is helpful!
Nicholas
>
> Temperature control:
> 1.
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen no ;# don't couple langevin bath to hydrogens
>
> 2.
> tcouple on
> tcoupletemp $temperature
>
> Pressure control:
> 1.
> useGroupPressure yes ;# needed for 2fs steps
> useFlexibleCell no ;# no for water box, yes for membrane
> useConstantArea no ;# no for water box, yes for membrane
>
> berendsenpressure on
> berendsenpressuretarget 1.01325
> berendsenpressurecompressibility 4.57e-5
> berendsenpressurerelaxationtime 100
> berendsenpressurefreq 10
>
> 2.
> useGroupPressure yes ;# needed for 2fs steps
> useFlexibleCell no ;# no for water box, yes for membrane
> useConstantArea no ;# no for water box, yes for membrane
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
> SurfaceTensionTarget 0.0 ;
>
>
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