Re: [AMBER] Does pmemd or pmemd.mpi support center of mass restraint?

From: Igor Marques <igor.dragon88.gmail.com>
Date: Fri, 13 Dec 2013 20:17:57 +0000

to the amber devs:

will pmemd.cuda support COM restraints in the near future?

many thanks,
igor




 Igor Marques, PhD Student
MSc in Pharmaceutical Biomedicine
BSc in Biomedical Sciences

Molecular Modeling Group University of
Aveirohttp://molecular-modeling.dq.ua.pt/

Mobile phone: +351 918 567 294
Landline: +351 234 247 254
Through PBX: +351 234 370 200 (ext. 22160)

Universidade de Aveiro
Campus Universitario de Santiago
Agra do Crasto Edificio 30
3810-193 Aveiro - Portugal



On Sat, Nov 30, 2013 at 4:42 PM, Jason Swails <jason.swails.gmail.com>wrote:

>
>
> On Nov 30, 2013, at 11:01 AM, zhongqiao hu <zhongqiao.hu.gmail.com> wrote:
>
> > As Ross suggested (http://archive.ambermd.org/201301/0155.html), pmemd
> > should support center of mass restraint. But I failed to use it.
> >
> > I want to put an angle restraint.
> > the mdin file is as follows
> > Stage equil
> > &cntrl
> > imin = 0, irest = 1, ntx = 5,
> > nstlim = 5000, dt = 0.002,
> > ntpr = 5000, ntwr = 5000, ntwx= 5000,
> > ntc = 2, ntf = 2,
> > cut = 10.0, ntb = 1,
> > temp0 = 310.0, ntt = 3, gamma_ln = 2.0,
> > ntp = 0, pres0 = 1.0, taup = 2.0,
> > nmropt = 1,
> > &end
> > &wt
> > type='DUMPFREQ', istep1=50,
> > &end
> > &wt
> > type='END',
> > &end
> > DISANG=disang_95.in
> > DUMPAVE=angle_95.dat
> >
> > the file disang_95.in is
> > Harmonic restraints for angle
> > &rst
> > iat=-1,-1,-1,
> > r1=-180.0, r2=95.0, r3=95.0, r4=180.0,
> > rk2=40000, rk3=40000,
> > igr1=1120,1134,1148,1164,1179,1203,1230,1236,
> > igr2=4850,4865,4885,4907,4919,4930,4949,4960,
> > igr3=7499,7506,7516,7540,7555,7561,7584,7590,
> > &end
> >
> > Whenever I used pmemd, it always immediately showed error:
> > At line 1008 of file nmr_calls.F90 (unit = 33, file = 'disang_95.in')
> > Fortran runtime error: Bad data for namelist object igr2
> >
> > If I remove the line "igr2=...." and change the line "iat=-1,-1,-1" to
> > "iat=-1,4850,-1", then it showed error:
> > At line 1008 of file nmr_calls.F90 (unit = 33, file = 'disang_95.in')
> > Fortran runtime error: Bad data for namelist object igr1
> >
> > pmemd only works after I totally removed center of mass restraint.
> >
> > But sander did run for center of mass restraint.
> >
> > I know pmemd.cuda does not support center of mass restraint. But does
> pmemd
> > support it or not? I am using amber12.
>
> Pmemd only supports COM for distance restraints.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
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Received on Fri Dec 13 2013 - 12:30:02 PST
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