Thanks!
Lekpa
On Tue, Sep 7, 2010 at 4:36 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> I do not think this is a problem.
> make sure you also use chirality retraints, not just cis/trans.
> I believe it is possible that people who did not use restraints might be
> ok,
> but they also might not have checked their results carefully. at 600K with
> Amber we find it happens very frequently.
>
> On Mon, Sep 6, 2010 at 7:37 PM, Lekpa Duukori <duukori.gmail.com> wrote:
>
> > Hi all,
> >
> > I have been running some REMD in explicit solvent and using gamma_ln=2.0,
> I
> > have however noticed that most of the papers I see use a value of 1.0 and
> I
> > was wondering if this can cause some problems if the thermostat is not
> very
> > strong. I just want to hear what people think about this. Also I see that
> > high temperature calculations (up to 600K) is reported in the literature
> > but
> > most do not state that restraints are used to avoid cis-trans
> > isomerisation,
> > is this the best thing to do?
> >
> > The following is a full input file one one replica
> >
> > &cntrl
> > imin = 0,
> > irest = 1,
> > ntx = 5,
> > ntb = 1,
> > cut = 10,
> > ntc = 2,
> > ntf = 2,
> > ntt = 3,
> > gamma_ln = 2.0,ig=20459,temp0=510.2,
> > nstlim = 125, dt = 0.002,
> > nmropt=1,
> > numexchg=40000,
> > ntpr = 250, ntwx = 250, ntwr = 1000,iwrap=1
> > /
> > &wt TYPE='END'
> > /
> > DISANG=model.MAKERST
> >
> >
> > Thanks
> >
> > Lekpa.
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Sep 07 2010 - 07:30:05 PDT
