Hi Ross,
thanks for the explanation. Let me re-interpret your email to make sure I
understand what you've mentioned...
1. I am using ntt=1 which does not use random numbers. Does that mean
whatever number I assign to ig, it doesn't matter at all? As long as I use
ntt=1, each run will always be identical? (all the rest just read .rst file
from last run)
2. If I change to ntt=3, I also need to change tempi to non-0, for instance
1 K, in order to use ig=-1. Right?
3. I don't have a specific reason to use ntt=1. If any, it might because I
learned and obtained input files from senior labmates... My system is a
very common, 100 residues, protein-small molecule complex. Currently in my
lab, I am using Amber 14. The final goal for these multiple independent
runs is to calculate binding energies. Can you give a common advice about
the ntt I should use for equilibrium and run under NPT? I found some
suggestion in tutorial (
http://ambermd.org/tutorials/basic/tutorial1/section3.htm) but it's for
NVT. Thank you very much!
-Guqin
2015-10-16 12:25 GMT-04:00 Ross Walker <ross.rosswalker.co.uk>:
> Hi Guqin,
>
> The behavior you see is correct. There is nothing in your simulation that
> is dependent on the random number stream.
>
> ntt=1 is the Berendsen barostat - this does not use random numbers, only
> ntt=2 and 3 use the random number stream. I'd suggest switching to ntt=3 if
> you don't have a specific reason for wanting to use Berendsen. That will
> then get you different simulations due to different random seeds.
>
> The other reason you don't see a dependence is because tempi=0 - Ad you
> noted the manual said ntx .lt. 3 AND TEMPI .ne. 0.0. You have ntx=1 but
> have tempi == 0.0. If you truly want different initial velocities then set
> tempi to a number greater than zero and you will get a boltzman
> distribution of velocities (based on the random number stream) to give you
> the initial temperature you set with tempi.
>
> Hope that helps.
>
> All the best
> Ross
>
> > On Oct 16, 2015, at 9:17 AM, Guqin Shi <shi.293.osu.edu> wrote:
> >
> > (I forgot to add [AMBER] in subject so I resend this email. Hope I didn't
> > cause any confusion.. Thanks!)
> >
> > Hi all!
> >
> > recently I want to do multiple independent runs by assigning different
> > velocities to each run.
> >
> > So I have three stages for each run, eq1 for heating up, eq2 for pressure
> > relaxation, and then run at NPT conditions. The assignment of velocites
> is
> > at eq1 stage and below is the input:
> >
> > *Heating up the system equilibration stage -- only water is mobile*
> > * &cntrl*
> > * nstlim=100000, dt=0.002, ntx=1, irest=0, ntpr=500, ntwr=5000,
> ntwx=500,*
> > * tempi =0.0, temp0=300.0, ntt=1, tautp=2.0, ig=-1,*
> > * ntb=1, ntp=0,*
> > * ntc=2, ntf=2,*
> > * nrespa=1,*
> > * ntr=1,*
> > * iwrap=1,*
> > */*
> > *Keep protein and ligand fixed*
> > *50.0*
> > *RES 1 100*
> > *END*
> > *END*
> >
> >
> > However, I noticed that each run are IDENTICAL in all .out, .crd, and
> .rst
> > files. So I realize the ig flag didn't work at all. Maybe I didn't fully
> > understand the sentence in manual "The MD starting velocity is dependent
> on
> > the random number generator seed if NTX .lt. 3 .and. TEMPI .ne. 0.0." Can
> > anybody help illustrate how to correctly use ig flag? It seems ig=-1
> > doesn't work if I have ntt=1 and tempi=0.0...? So in my case, what's the
> > best way to assign random velocities in each run? How about assigning a
> > number to ig? Do I need to change it for each run? It should be a very
> > simple one but I have no experience dealing with it before.. Thanks for
> > your time!
> >
> > Best,
> > Guqin
> >
> > --
> > Guqin SHI
> > The Ohio State University
> > College of Pharmacy
> > 500 W. 12th Ave.
> > Columbus, OH, 43210
> > (614)688-3531
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Guqin SHI
The Ohio State University
College of Pharmacy
500 W. 12th Ave.
Columbus, OH, 43210
(614)688-3531
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Received on Fri Oct 16 2015 - 10:00:03 PDT
