From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Mon Oct 18 2010 - 11:32:18 CDT
Hi Mingjun,
I just want to be sure you're reporting the actual simulation cell volume
and not the bounding box of the solvent without coordinate wrapping.
If all you want is a random unfolded protein just do NVT as others have
suggested, since both pressure and temperature will induce unfolding.
-Jim
On Sun, 17 Oct 2010, 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?
>
>
> 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 ;
>
>
>
> Many thanks.
>
> Mingjun
> ________________________________________
> From: Nicholas Musolino [musolino_at_mit.edu]
> Sent: Sunday, October 17, 2010 9:29 PM
> To: mjyang
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: expansion of solvation box at high temperature
>
> Dear mjyang:
>
> On Oct 17, 2010, at 3:03 AM, mjyang wrote:
> I performed a simulation of a protein + TIP3 water system at 600K. But after 2 ns production run under NPT ensemble, the volume of solvation box expanded by more than 1000 times and the mass density reduced from 1.05909 g/cm^3 to 0.000607189 g/cm^3. I am not sure whether this phenomenan is caused by NPT ensemble at hight temperature or any other factors
>
> Your system vaporized. Boiled! So you're right about the cause being high temperature.
>
> To provide helpful advice, we will need to see you pressure control parameters, and your temperature control parameters, from your NAMD input file.
>
> Did you gradually heat up to 600 K from a low temperature? Or just set the thermostat there, and run? The first option will usually be more stable, in practical terms.
>
> Also, can you share why you're trying to simulate at 600 K? Is this for some kind of simulated annealing procedure?
>
> Thanks and good luck,
> Nicholas Musolino
> -----
>
> ----------------------------------------------------------------------
> Nicholas Musolino
> Ph.D. candidate, Department of Chemical Engineering, MIT
> musolino_at_mit.edu<mailto:musolino_at_mit.edu> | 617-253-6675 | Room E19-528
>
>
>
>
>
>
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