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

From: Ross Walker <ross.rosswalker.co.uk>
Date: Fri, 13 Dec 2013 12:25:18 -0800

Hi Igor,

It is planned for AMBER 14 (the next version of AMBER, we are skipping 13).

All the best
Ross


On 12/13/13 12:17 PM, "Igor Marques" <igor.dragon88.gmail.com> wrote:

>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 - 12:30:03 PST
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