AMBER Archive (2007)

Subject: Re: AMBER: Problem with Getting SHAKE to work

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Sat Sep 15 2007 - 22:16:10 CDT

Update: it appears that the problem concerns only SPC/E water, glycerol,
acetate, and ammonium residues in the simulation--hydrogen bonds on the
protein are being constrained. The frcmod.spce file in the AMBER9
distribution is being referenced, so I'm not sure why the SPC/E water
geometry is getting screwed up. I am using .prp and .frcmod files for
glycerol, ammonium, and acetate, however, so perhaps there's something in
those that I did not sufficiently specify to let AMBER know that some atom
is indeed a hydrogen.

Dave

On Sat, 15 Sep 2007, David Cerutti wrote:

> Hello,
>
> I was under the impression that all I had to do to turn on SHAKE in a
> pmemd dynamics run was set ntf = 2 and ntc = 2; however, when I do this I
> find that bonds containing hydrogen are still fluctuating. This creates
> problems, of course, when polar hydrogens come too near a negatively charged
> atom and cause the simulation to crash.
>
> Here is my input file. Can anyone suggest a remedy?
>
>>>>>>
> Round 1 of MD equilibration
> &cntrl
>
> nmropt = 0,
> ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
> ntpr = 100, ntwx = 1000, ntwv = 0, ntwe = 100,
> iwrap = 1, ioutfm = 0,
>
> ntf = 2, ntb = 1,
> cut = 9.0,
>
> ibelly = 1, ntr = 0,
>
> imin = 0,
> nstlim = 100000,
> nscm = 1000,
> t = 0.0, dt = 0.0005,
>
> temp0 = 293.0, tempi = 0.0,
> ig = 9376841,
> ntt = 3,
> gamma_ln = 3.0,
> vlimit = 20.0,
>
> ntp = 0, pres0 = 1.0, comp = 44.6,
> taup = 1.0,
>
> ntc = 2, tol = 0.001, watnam = 'WAT ',
>
> &end
> Group input for restraint mask
> FIND
> SEARCH
> ATOM 1 29008
> END
> END
> <<<<<
>
> Thanks!
>
> Dave
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