Hi, Chen
It's easy to modify mm_pbsa.pl to use MPI. For example, modify the
following line s in mm_pbsa_calceneent.pm
$command = $r_pro->{"SANDER"} . " -O" .
to
$command = "mpirun -np 1" . $r_pro->{"SANDER"} . " -O" .
Another more convenient way is to specify the serial SANDER program in
mmpbsa.in input file.
.PROGRAMS
SANDER path_to_sander_serial
You can search the archive for more detailed discussions. I hope this
helps.
Regards!
Liu
On Sat, 30 Jul 2005 09:09:13 +0800, Wei Chen <gtg553p.mail.gatech.edu>
wrote:
> Hi, Liu,
>
> I am a new user for amber. Do you know how to modify mm_pbsa.pl or
> use serial SANDER?
>
> Thank you!
>
> Wei Chen
>
>
> 引用 JunJun Liu <ljjlp03.gmail.com>:
>
>> Dear Chen:
>>
>> if you didn't modify the mm_pbsa.pl script to use MPI, I think you need
>> to
>> use the single processor version of SANDER.
>>
>> regards!
>>
>> Liu
>>
>> On Sat, 30 Jul 2005 08:55:07 +0800, Wei Chen <gtg553p.mail.gatech.edu>
>> wrote:
>>
>> > Hi,
>> >
>> > I even got samder_com.1.out file. I think maybe somthing wrong with
>> > mpirun.
>> >
>> > Thanks!
>> >
>> > Wei Chen
>> >
>> > 寮曠敤 Suxin Zheng <sxzheng.u.washington.edu>:
>> >
>> >> You should look the sander_com.1.out to see the problem, whether the
>> >> top or the crd file is fited correctly.
>> >>
>> >> On Jul 29, 2005, at 5:10 PM, Wei Chen wrote:
>> >>
>> >> > Hi,
>> >> >
>> >> > When I ran mm_pbsa.pl xxx in amber8, some errors occur as follow:
>> >> >
>> >> > mpirun must be used to launch all MPI applications
>> >> > /gt/lib1/Library/amber8/exe/sander -O -i sander_com.in -o
>> >> > sander_com.1.out -
>> >> > c ./hFc1_CD16B_na2_com.crd.1 -p ./hFc1_CD16B_na2_minimize.prmtop
>> >> > not successful
>> >> >
>> >> > Anybody knows how to solve this problem?
>> >> >
>> >> > Wei Chen
>> >> >
>> >> > --
>> >> >
>> >> >
>> ----------------------------------------------------------------------
>> >> > -
>> >> > The AMBER Mail Reflector
>> >> > To post, send mail to amber.scripps.edu
>> >> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>> >> >
>> >>
>> >>
>> >>
>> ----------------------------------------------------------------------
>> >> Suxin Zheng
>> >> Research Associate
>> >> Box 351700
>> >> Department of Chemistry, University of Washington
>> >> Seattle, WA, 98195-1700
>> >> sxzheng.u.washington.edu
>> >>
>> >>
>> >>
>> >>
>> -----------------------------------------------------------------------
>> >> The AMBER Mail Reflector
>> >> To post, send mail to amber.scripps.edu
>> >> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>> >>
>> >
>> >
>>
>>
>>
>> --
>> JunJun Liu
>>
>> College of Chemistry
>> Central China Normal University
>> WuHan 430079
>> P.R. China
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>>
>
>
--
JunJun Liu
College of Chemistry
Central China Normal University
WuHan 430079
P.R. China
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Received on Sat Jul 30 2005 - 03:53:01 PDT
