Re: [AMBER] constant pressure

From: Yong Duan <>
Date: Mon, 05 Dec 2011 21:28:17 -0800

Yes, those messages are alright.

To tell you the truth, in normal systems, these are totally unnecessary.
My typical protocol is to heat to 300K immediately after energy
minimization. However, your system seems very unstable. So, I just want to
be extra cautious.

Please change

nstlim=200000, ntx=7, ntc=2, iwrap=1,

Let's do it step-by-step. Let the system continue from the one you just
finished for 100 ps at 50K. After that, we can raise the temperature to

The key here is to have ntc=2. This is necessary since you are using
water. The typical water models, SPC, SPCE, TIP3P, TIP4P, etc., were all
designed with fixed bond lengths. Therefore, if you do not use ntc=2, you
actually use wrong water models. And, because the hydrogen atoms in
SPC/SPCE/TIP3P/TIP4P have no van der Waals radius, if you set ntc=1, bond
would be the only force that prevents them from moving too close to
another negatively charged atom (an ion, for instance). This energy
barrier is small and works only at low temperature and very small time
step. When you set ntc=2, you use van der Waals energy of the oxygens to
prevent the water hydrogen from moving too close to a negatively charged

Yong Duan, Ph.D, Professor
UC Davis Genome Center and
Department of Biomedical Engineering
University of California at Davis
Davis, CA 95616
On 12/5/11 3:18 PM, "kirtana S" <> wrote:
>Thank you all for the help and suggestion made .
>According to the suggestions of Prof Duan after running constant volume
>then using single processor due to density of my system in constant
>pressure  the simulation runs with some statements as
>check COM velocity, temp:   0.000220 0.00 (Removed)  in my out file .
>are these alright to proceed. My constant pressure input file below
>   imin=0, ntx=5,
>   irest=1, ntxo=1,tempi=50.0,
>   ntf=1, ntc=1,
>   ntpr=1000, ntwx=1000, ntwe=1000,
>   nstlim=1500000,tautp=1, temp0=50.0,
>   dt=0.0005, nscm=100,
>   ntb=2,ntp=1,
>   ntt=1, nsnb=20,
> &end
>My other question is I have equilibrated the system at 50K . Whereas my MD
>run is to be done at 300K . So should I repeat these steps to gradually
>raise the temperature to 300K at constant  volume. Again while heating
>should I need to have restraints on the residues (or solute) I am using
>present run for a bigger system , I can send the output files again if
>Thanks for your time
>On Mon, Dec 5, 2011 at 8:19 AM, David A Case
>> On Sun, Dec 04, 2011, Brian Radak wrote:
>> > Minimization usually (always?) ignores PBCs.
>> This is not correct; just noting that to prevent further confusion in a
>> long
>> thread.
>> There should be no need to minimize between doing a constant volume and
>> constant pressure equilibration.  In fact, the safest thing to do is to
>> make sure irest=1 (so you are continuing from a previous run), and that
>> only change to the input is from ntb=1,ntp=0 --> ntb=2,ntp=1.  In the
>> constant
>> pressure run, set ntpr=1 and nstlim=50, and make sure that the energies
>> the
>> first step of the constant pressure run match those at the last step of
>> NVT equilibration.  [I'm wondering if there is some problem with how you
>> are
>> naming the input files--be sure that restart file from the previous
>>step is
>> indeed used as the input file for the next step.]
>> ....dac
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Received on Mon Dec 05 2011 - 21:30:04 PST
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