Re: expansion of solvation box at high temperature

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Sun Oct 17 2010 - 12:25:19 CDT

If your goal is just to initialize a set of unfolded structures to then run folding simulations, there might be easier ways to do this, rather than running an unfolding trajectory at high temperatures. For example, you could start with random coil conformations from the unfolded state using the method in Jha et al., PNAS (2005) PMID: 16131545, for which there is a webserver that will generate models for you:
http://godzilla.uchicago.edu/cgi-bin/unfolded.cgi

Alternatively you could run a monte carlo simulation in the space of the backbone dihedrals as was done by Voelz, et al. JACS (2010) PMID: 20070076 (see the Supplementary Materials), and then solvate the resulting conformation.

If you are set on using high temperature unfolding simulations, I would also check that the system has actually reached each of your intermediate temperatures before you raise it again to ensure that you are gently heating the system rather than just blowing it up.

Best of luck,
Josh

On Oct 17, 2010, at 11:27 AM, Nicholas Musolino wrote:

> 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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