Thanks for feedback Rahull.
Since both types work independently in pmemd, I guess only minor changes
are required to make the combination also work :-) To the developers: is
it hard to make the combination of both restraint types work in
pmemd(.cuda)?
Thanks,
JP
On 04/23/2013 03:32 PM, Rahul Banerjee wrote:
> Hi Jan-Philip,
>
> This combination works with Sander but not with PMEMD.
>
> I do not understand though, why this option is not available. When NMR restraints can be reduced gradually, why not positional restraints?
>
> With best regards,
> Rahull
> ________________________________________
> From: Jan-Philip Gehrcke [jgehrcke.googlemail.com]
> Sent: Monday, April 22, 2013 5:11 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Reducing positional restraint gradually
>
> Rahul,
>
> I cannot answer your question, but have another one: you are combining
> ntr=1/restraintmask-based restraints with nmropt=1-based restraints. I
> vaguely remember that pmemd does not support this combination, i.e. that
> it only supports one of these at the same time. Is that still the case,
> do you run the simulation with sander?
>
> Cheers,
>
> Jan-Philip
>
>
>
> On 22.04.2013 21:11, Rahul Banerjee wrote:
>> Dear Amber users,,
>>
>> I am running equilibration simulation in presence of a finite positional restraint on all heavy atoms of my system. How can I reduce the restraint force gradually in 1000 steps? My reference structure is the starting structure of the simulation. I am using following script below. At the final step the restraint energy should be zero as the 'k' goes to zero. But it is not so. Am I wrong conceptually?
>>
>> With best regards,
>> Rahul
>>
>> Equil
>> &cntrl
>> imin=0,irest=0,ntx=1,
>> nstlim=1000,dt=0.002,
>> ntc=2,ntf=2,
>> cut=10.0, ntb=2, ntp=1, taup=2.0,
>> ntwe=5, ntpr=5, ntwx=5, ntwr=5,
>> ntt=3, gamma_ln=2.0, ig=-1
>> temp0=300.0, nmropt=1,
>> ntr=1, restraintmask=':1-120&!.H=', restraint_wt=8.0,
>> /
>> &wt
>> TYPE='REST', istep1 =0, istep2 = 1000,
>> value1 = 8.0, value2 = 0,
>> /
>> &wt type = 'END'
>> /
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>>
>
>
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Received on Tue Apr 23 2013 - 07:30:03 PDT
