Just to follow up on this - is it possible to apply distance restraints with pmemd or only with sander?
>From my reading of the manual it is only with sander.
Thanks,
Dan
> On Jan 14, 2022, at 9:55 PM, David A Case <david.case.rutgers.edu> wrote:
>
> On Fri, Jan 14, 2022, Daniel Burns wrote:
>>
>> prod
>> &cntrl
>> imin=0, irest=1, ntx=5, iwrap=1,
>> nstlim=15000000, dt=0.002,
>> ntc=2, ntf=2,
>> cut=10.0, ntb=2, ntp=1, taup=1.0,
>> ntpr=2000, ntwx=2000, ntwr= 2000,
>> ntt=3, gamma_ln=2.0, temp0=303.15,
>> ntr = 1, restraintmask =":479<:5&!.H=",
>> restraint_wt = 1.0, nmropt=1,
>> &end
>> &wt type='REST', istep1=0, istep2=10000000, value1=1.0, value2=0.0, &end
>> &wt type='REST', istep1=10000001, istep2=15000000, value1=0.0, value2=0.0, &end
>> &wt type='END' &end
>
> Oh, my. It may be that the REST in the &wt namelist doesn't mean what you
> think it does. These refer to "NMR restraints"
> (bonds/angles/torsions/etc.). But you don't appear to have defined any such
> restraints.
>
> The "restraint_wt" and "restraintmask" refer to Cartesian restraints that
> keep the atoms near to their positions in the reference structure. There is
> no way to have restraint_wt depend upon step number.
>
> I can see how easy it would be to confuse two things that have such similar
> names. At a minimum, we need to add an explicit warning to the manual.
> Changing "restraint_wt" to something like coordinate_restraint_wt" would
> help, but would have a big backwards-incompatibility downside. Volunteers
> are solicited to pitch in to make this better.
>
> ....dac
>
>
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Received on Sat Jan 15 2022 - 11:00:02 PST
