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 - 13:29:35 CDT

as I said before, this result seems perfectly acceptable to me. what is the
density of water at 600K/1atm? pretty low. reducing step size
and relaxation time will not change that, only switching to NVT will
(or using a huge value for the target pressure, check the experimental
data to see what pressure is needed to keep water a liquid at 600K).

what happened during your constant volume simulation that you ran?
carlos

MURAT CETINKAYA wrote:

>I checked every tutorial and other responses about my problem. I tried to half
>the step size (i.e. 0.0005 fs) and increase the time of solvent relaxation
>(from 100 to 200ps).
>Btw, the initial density of the system is 0.80 and sander terminates around
>0.69.
>
>I will try other suggestions.
>
>Thanks for all your help,
>
>Murat CETINKAYA
>
>On Mon, 18 Oct 2004 10:47:58, Bill Ross wrote:
>
>
>
>>>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
>>>
>>>
>>Have you seen the amber web material on equilibration?
>>
>>
>>
>>>I am also aware that the density continuously falls
>>>during the constant pressurerun.
>>>
>>>
>>If the density is approaching 1.0, then this is what you want.
>>
>>Bill
>>
>>
>>
>>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu