AMBER Archive (2004)

Subject: Re: AMBER: const-P MD at high T

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Oct 18 2004 - 12:22:48 CDT

then you might want to keep the volume from 300K and increase the T.
you might want to try something not too high, though, like 350K or 400K.
At 600K, you'll have to consider things like reducing the integration
time step, putting restraints on peptide bonds and chirality, and so on.
those
will cause problems even at constant volume.

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

MURAT CETINKAYA wrote:

>We had some unusual behaviors of our protein at 300K so we want to see if it
>also happens at higher temperatures. Maybe, simulating in vacuum can solve the
>problem.
>
>Thanks,
>Murat
>
>On Mon, 18 Oct 2004 12:25:52 +0000, Carlos Simmerling wrote:
>
>
>
>>it seems to me that at 600K and 1atm the system is in the gas
>>phase, so to me this seems like what I would expect. why are
>>you running at 600K? not to match 600K experiment, so maybe
>>what you want is to use contant volume at that temperature.
>>carlos
>>
>>===================================================================
>>Carlos L. Simmerling, Ph.D.
>>Associate Professor Phone: (631) 632-1336
>>Center for Structural Biology Fax: (631) 632-1555
>>Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
>>Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
>>===================================================================
>>
>>
>>
>>
>>MURAT CETINKAYA wrote:
>>
>>
>>
>>>Dear Amber users,
>>>
>>>I am trying to run 1ns simulations on my explicitly solvated protein system.
>>>
>>>
>But
>
>
>>>when I try to run sander with high system temperatures (more then 500K)sander
>>>gives out an error saying that:
>>>
>>> volume of ucell too big, too many subcells
>>> list grid memory needs to be reallocated, restart sander
>>>
>>>I am also aware that the density continuously falls during the constant
>>>
>>>
>pressure
>
>
>>>run. I have performed constant volume runs (prior to const P run)for at least
>>>100ps (even tried 200ps) but I still get the same result. Here is my input
>>>file:
>>>
>>>&cntrl
>>> imin = 0, irest = 1, ntx = 7,
>>> ntb = 2, pres0 = 1.0, ntp = 1,
>>> taup = 20.0,
>>> cut = 10, ntr = 0,
>>> tempi = 600.0, temp0 = 600.0,
>>> ntt = 1,
>>> nstlim = 1000000,
>>> ntpr = 5000, ntwx = 5000, ntwr = 5000
>>>/
>>>
>>>
>>>Any kind of help really appreciated...
>>>Thanks,
>>>
>>>Murat Cetinkaya
>>>PennState Univ, UP
>>>
>>>
>>>
>>>
>>>
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