Hi, this happened to me too. Once I set "step 2" to run with 2 cpus, it
worked fine. Not sure what your problem is about, but I have included my
settings. Hope this might help. :)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
cat << EOF > mdin_min_v0_l${X} # change settings
density minlibration
&cntrl
imin = 1, ntx = 1, ntmin=2,
maxcyc=500,
ntpr = 1,
ntf = 1, ntc = 1,
ntb = 1, cut = 9.0,
icfe=1, clambda = 0.${X},
EOF
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
#################
On 19 March 2011 05:43, Dian Jiao <oscarjiao.gmail.com> wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Mar 19 2011 - 12:00:05 PDT
