Re: [AMBER] TI simulations

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Fri, 1 May 2020 12:27:21 +0000

Thanks so much Dr Lin.
Debarati

From: Song, Lin<mailto:songlin3.chemistry.msu.edu>
Sent: 30 April 2020 20:18
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] TI simulations

Hi Debarati,

In short, ntwv is an option about writing the velocities to the trajectory file; ntave is the number of steps used to calculate the average energies; ntp specifies whether to use NPT simulation, the default value of pres0 is 1.0 bar, which is around 0.987 atm.

Here is the AMBER manual, where you can find the detailed explanations for these keywords: https://ambermd.org/doc12/Amber19.pdf

Best,
Lin

On Apr 30, 2020, at 3:09 PM, Debarati DasGupta <debarati_dasgupta.hotmail.com<mailto:debarati_dasgupta.hotmail.com>> wrote:

I came across a sample input file from Prof Kenneth Merzís group and it is an equilibration input file. These are the contents:
I have 3 queries:


What is the utility of setting ntwv =1 ? ( have never tinkered with this parameter in AMBER ever)
Also the same query about ntave=10 (What is the importance of ntave parameter)
If we do not mention press0=1, will it not be the default value. I thought ntp =1 means we are setting the pressure at 1 atm.

Thanks



NPT MD w/No position restraints and PME (sander)
&cntrl
 ntx = 5,
 irest = 1,
 ntpr = 1000,
 ntwx = 1000,
 ntwe = 1000,
 ntwr = 1000,
 ig = -1,

 ntf = 1,
 ntb = 2,
 ntp = 1, pres0 = 1.0, taup = 2.0,gamma_ln = 2.0,
 cut = 9.0,
 iwrap = 1,
 nsnb = 10,

 nstlim = 1000000,
 t = 0.0,
 nscm = 1000,
 dt = 0.001,

 temp0 = 300.0,
 tempi = 300.0,
 ntt = 3,
 tautp = 2.0,

 ntc = 1,
 iwrap=1, ioutfm=1, ntwv=-1,ntave=1000,
 icfe = 1, ifsc = 1,
 timask1=':1',
 timask2=':2',
 scmask1=':1.CB,HB1,HB2,HB3,',
 scmask2=':2.CK1,CK2,NK1,CK3,NK2,CK4,HK1,HK2,HK3,',
 clambda=0.5,
&end
&ewald
  skinnb=2, nfft1=96, nfft2=96, nfft3=96,
/



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Received on Fri May 01 2020 - 05:30:03 PDT
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