Re: expansion of solvation box at high temperature

From: Jeffrey Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Sun Oct 17 2010 - 11:44:53 CDT

  The "problem" is you are attempting to run a simulation on a
meta-stable system. At 600 K, the vapor pressure of water is 123.5
bar. You are running a simulation at 600 K and 1.0 bar. Therefore the
simulation is doing what it should do, become a gas phase. You have a
secondary problem that at 600 K, the TIP3P water model does not predict
the vapor pressure of water correctly. Even if you run at 123.5 bar,
you may not get the correct density; you might still end up with a gas
phase.

Your best bet is to set the density of water to whatever it needs to be
and run NVT simulations.

Regards,
Jeff

On 10/17/2010 11:56 AM, mjyang wrote:
> Hi Nicholas,
> Many thanks for your time.
> Maybe, it works for a larger value of pressure or just under NVT ensemble.
> But I am not sure about these points and require more tests.
> Any other comments about fixing this problem is appreciated.
>
> Many thanks.
>
> Mingjun
>
> ________________________________________
> From: Nicholas Musolino [musolino_at_mit.edu]
> Sent: Sunday, October 17, 2010 11:27 PM
> To: mjyang
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: expansion of solvation box at high temperature
>
> 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 ;
>>
>>

-- 
======================================================================
Jeffrey J. Potoff			  jpotoff_at_chem1.eng.wayne.edu
Associate Professor			  Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr			  Phone:(313)577-9357		
Detroit, MI 48202  	                  Fax:  (313)578-5815
http://potoff1.eng.wayne.edu
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