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 Merz’s 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
