Again,
as you mentioned I can use position restrain with PMEMD.cuda. I guess
heating the system with this script is OK ?
Heating the system linearly with weak restraints
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
taup = 2.0,
cut = 10,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
ig = 2342,
gamma_ln = 1.0, nmropt = 1,
nstlim = 50000, dt = 0.002
ntpr = 100, ntwx = 100, ntwr = 50000
/
&wt TYPE='TEMP0', istep1=0, istep2=40000,
value1=0.1, value2=300.0, /
&wt TYPE='DUMPFREQ',ISTEP1=10, /
&wt TYPE='END' /
Keep protein fixed
5.0
RES 1 367
RES 385 410
END
END
On Tue, Aug 12, 2014 at 4:30 PM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
wrote:
> Thanks Jason
>
>
>
>
> On Tue, Aug 12, 2014 at 4:17 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> On Tue, Aug 12, 2014 at 10:09 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
>> wrote:
>>
>> > Hi,
>> > I checked that ibelly is not applicable with PMEMD so in order to put
>> > restrain on my protein during minimization and heating, I am using
>> > sander.MPI ..
>> >
>> > And once it is equilibrated, I used PMEMD.cuda to run the actually
>> > production. Is it acceptable ?
>> >
>>
>> Yes.
>>
>> As a side note, you can often use positional restraints instead of belly
>> to
>> keep atoms fixed to a certain spot with a spring constant while still
>> allowing it to jiggle a _little_. This is more common in my experience
>> than using belly, but YMMV.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Tue Aug 12 2014 - 08:00:03 PDT
