Hi Brian,
Center of mass necessarily requires some kind of all to all communication
in parallel - even if you hide this with a binary tree or something
similar, so it has to be programmed carefully to get good performance.
Ultimately the rate limiting step right now though is manpower pure and
simple.
All the best
Ross
On 10/8/13 10:30 AM, "Brian Radak" <radak004.umn.edu> wrote:
>The error message says it all. PMEMD does not support all of the same
>restraints as SANDER.
>I believe the center of mass restraints are the ones not implemented.
>
>Regards,
>Brian
>
>P.S. To developers: Is there an implementation/performance reason for this
>difference in features or is it just because coding up all of those
>difference restraints involves a lot of time and effort for something so
>specialized and rarely used?
>
>
>On Tue, Oct 8, 2013 at 1:21 PM, Sourav Purohit <sour000.gmail.com> wrote:
>
>> Hi,
>>
>> I am using the following restraint file to restrain a dihedral and two
>> distances.
>>
>>
>> &rst
>> iat=393,399,239,234,
>> r1=-30.0, r2=150.0, r3=150.0, r4=320.0,
>> rk2=300.0, rk3=300.0,
>> &end
>>
>> &rst
>> iat= -1, -1,
>> igr1= 11,12,14,15,16,17,18,20,21,24,25,26,28,31,
>>
>> 234,235,237,239,240,243,244,245,246,248,251,
>> igr2=
>>
>>
>>360,361,363,365,366,369,370,371,372,374,377,389,390,392,393,394,395,396,3
>>98,399,402,403,404,406,409,
>> r1=-5.0, r2=2.5, r3=2.5, r4=10.0,
>> rk2=400.0, rk3=400.0,
>> &end
>>
>> &rst
>> iat= -1, -1,
>> igr1=
>>
>>
>>106,108,109,111,113,114,117,118,119,120,122,125,137,138,140,141,142,143,1
>>44,146,147,150,151,152,154,157,
>> igr2=
>>
>>
>>263,264,266,267,268,269,270,272,273,276,277,278,280,283,486,487,489,491,4
>>92,495,496,497,498,500,503,
>> r1=8.8 ,r2=22.0 ,r3=22.0 ,r4=35.0,
>> rk2=300.0 rk3=300.0,
>> &end
>>
>> Here igr1 and igr2 contain atom nos. , the distance between whoes COM
>>is to
>> be restrained
>>
>> When i try to apply these restraints in PMEMD I get the following error.
>>
>> *"PMEMD only supports atom groups in distance restraints!*
>> *Please use SANDER instead!"*
>>
>>
>> *Kindly tell the reason for this. Is the restraint definition wrong?*
>> *
>> *
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
>--
>================================ Current Address =======================
> Brian Radak : BioMaPS
>Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
>University of New Jersey
> University of Minnesota - Twin Cities : Center for
>Integrative
>Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
>08854-8066
> radak004.umn.edu :
>radakb.biomaps.rutgers.edu
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Received on Tue Oct 08 2013 - 11:00:05 PDT
