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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>
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Received on Tue Sep 07 2010 - 04:00:03 PDT
