Thanks for your reply, but have a question about your answer.
I used restraint of solutes for first 20ps (heating up from 0 to 298K).
But, after that, when I started MD at the starting point of 20ps, I
didn't apply restraints to solute molecules, so we see that restraint=0
at 32ps. I cannot understand why this problem is related to restraints
of solutes because I'm not using restraints after 20ps.
Thanks for your help in advance.
best,
Hwankyu.
On May 24, 2005, at 2:12 PM, Thomas E. Cheatham, III wrote:
>
>> I put wrong info about 20ps point. here, I attach 20ps energies again.
>> I really apologize for my mistake.
>> In 20ps, it has 299.88, which looks like reasonable temp.
>> could you look at this one more time?
>> -------------------------------
>> check COM velocity, temp: 0.002858 0.01(Removed)
>>
>> NSTEP = 10000 TIME(PS) = 20.000 TEMP(K) = 299.88
>> PRESS =
>> 0.0
>> Etot = -201648.0152 EKtot = 50211.0109 EPtot =
>> -251859.0262
>> BOND = 898.2060 ANGLE = 2473.6478 DIHED =
>> 1351.3450
>> 1-4 NB = 826.9863 1-4 EEL = -10156.4761 VDWAALS =
>> 32172.4335
>> EELEC = -280549.9268 EHBOND = 0.0000 RESTRAINT =
>> 1124.7582
>
> If this is correct, and you are indeed running with restraints (as
> pointed
> out on this reflector many times if you search the archive), likely you
> have a force constant that is too large leading to SHAKE failure. Try
> using a force constant for the restraints of less than 5 kcal/mol.
> Note
> that 1000 kcal/mol of restraint energy is a lot so make sure that you
> are
> restraining to what you want to be restraining too...
>
>
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Received on Tue May 24 2005 - 19:53:00 PDT
