Hi,
I am running TI minimization with softcore using Amber 10. My two input
files look like this:
mdin_v0
*minimization*
* &cntrl*
* imin=1,maxcyc=500,*
* cut=9,ntb=1,*
* icfe=1,clambda=0.2,*
* ifsc=1,ntmin=2*
* scmask=':1',crgmask=':1',*
* / *
mdin_v1
*minimization*
* &cntrl*
* imin=1,maxcyc=500,*
* cut=9,ntb=1,*
* icfe=1,clambda=0.2,*
* ifsc=1,ntmin=2*
* scmask='',crgmask='',*
* / *
At first I was using 4 CPUS and got this error:
*SANDER BOMB in subroutine imin > 0 and numtasks > 1*
* TI minimizations cannot be performed with > 2 CPUs*
So I changed it to 2 CPUS
*mpirun -n 2 sander.MPI -O -ng 2 -groupfile group_min*
In the v0 output file, it stops printing after the following and there is no
error messege.
*
--------------------------------------------------------------------------------
*
* 3. ATOMIC COORDINATES AND VELOCITIES*
*
--------------------------------------------------------------------------------
*
*
*
*LIG1
*
* begin time read from input coords = 80.000 ps*
*
*
* Number of triangulated 3-point waters found: 426*
*
*
As for v1 output, only the first line is printed out
* -------------------------------------------------------*
* Amber 10 SANDER 2008*
* -------------------------------------------------------*
The job is still running, just no output any more.
However the TI minimization works just fine for charge-removing step with
ifsc=0 on the same cluster. I can even use up to 8 cpus for one job.
Has this occurred to anyone? How do I deal with softcore minimization?
Thanks in advance.
~Dian
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Received on Fri Mar 18 2011 - 23:00:04 PDT
