Dear Amber users,
Again i got the same error of "segmentation fault" even whatever i modified
my batch-file. The "ndm_md1.rst" was not even created.
I compared the "ndm_md1.out" with other successful runs (i.e other
"xx_md1.out"), i found that the process of running wat-md1.in was halted in
the first step, as shown below (this is extracted from the "ndm_md1.out"):
*NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
Etot = -64769.2683 EKtot = 0.0000 EPtot =
-64769.2683
BOND = 79.7941 ANGLE = 500.8945 DIHED =
1498.9190
1-4 NB = 453.3799 1-4 EEL = 7256.7348 VDWAALS =
10279.1689
EELEC = -84838.1594 EHBOND = 0.0000 RESTRAINT =
0.0000
Ewald error estimate: 0.8471E-04
------------------------------------------------------------------------------
*
Please help. I really have no idea what is going on. I think the
"ndm_md1.rst" had not been created because the process stopped unexpectedly.
Thank you.
Chinsu
On Mon, May 16, 2011 at 7:46 PM, Chinh Su Tran To
<chinh.sutranto.gmail.com>wrote:
> Dear Jason,
>
> This is my batch file:
>
> */usr/local/amber10/exe/sander -O -i ./file-in/wat-min1.in -o
> ./results/ndm_min1.out -p ./results/ndm-wat.prmtop -c
> ./results/ndm-wat.inpcrd -r ./results/ndm_min1.rst -ref
> ./results/ndm-wat.inpcrd
>
> /usr/local/amber10/exe/sander -O -i ./file-in/wat-min2.in -o
> ./results/ndm_min2.out -p ./results/ndm-wat.prmtop -c ./results/ndm_min1.rst
> -r ./results/ndm_min2.rst
>
>
> /usr/local/amber10/exe/sander -O -i ./file-in/wat-md1.in -o
> ./results/ndm_md1.out -p ./results/ndm-wat.prmtop -c ./results/ndm_min2.rst
> -r ./results/ndm_md1.rst -x ./results/ndm_md1.mdcrd -ref
> ./results/ndm_min2.rst
>
> /usr/local/amber10/exe/sander -O -i ./file-in/wat-md2.in -o
> ./results/ndm_md2.out -p ./results/ndm-wat.prmtop -c ./results/ndm_md1.rst
> -r ./results/ndm_md2.rst -x ./results/ndm_md2.mdcrd
>
> /usr/local/amber10/exe/ambpdb -p ./results/ndm-wat.prmtop <
> ./results/ndm_md2.rst > ./results/ndm_md2.pdb*
>
> And the part below is the error I got:
>
>
> **/var/spool/torque/mom_priv/*
> *jobs/5731.bircibm.SC <http://5731.bircibm.sc/>: line 17: 14885
> > Segmentation fault /usr/local/amber10/exe/sander -O -i ./file-in/
> > wat-md1.in -o ./results/ndm_md1.out -p ./results/ndm-wat.prmtop -c
> > ./results/ndm_min2.rst -r ./results/ndm_md1.rst -x
> ./results/ndm_md1.mdcrd
> > -ref ./results/ndm_min2.rst
> >
> > Unit 30 Error on OPEN:
> > ./results/ndm_md1.rst
> > /var/spool/torque/mom_priv/**jobs/5731.bircibm.SC<http://5731.bircibm.sc/>:
> line 25:
> > ./results/ndm_md2.rst: No such file or directory
>
> *
> I double-checked and found that the ndm_md1.rst was not created, causing
> the next command was not performed, so the second error led to "could not
> open the ndm_md2.rst"
>
> I viewed other threads from Amber archive titled "segmentation fault"
> saying about "molecular size", but i dont think this error was addressed
> because i ran the similar batch file for other larger molecules and they ran
> fine.
>
> Is it possible that it was related to the TIP3PBOX of solvent I used? I
> used TIP3PBOX 12 for this molecule.
>
> Thanks for your reply, and hope more help.
>
> Chinsu
>
>
> On Mon, May 16, 2011 at 7:27 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> On Mon, May 16, 2011 at 6:42 AM, Chinh Su Tran To
>> <chinh.sutranto.gmail.com>wrote:
>>
>> > Dear Amber users,
>> >
>> > Below is the error I encountered when running a batch file of sander for
>> MD
>> > runs following 2-step minimization:
>> >
>> > */var/spool/torque/mom_priv/jobs/5731.bircibm.SC: line 17: 14885
>> > Segmentation fault /usr/local/amber10/exe/sander -O -i ./file-in/
>> > wat-md1.in -o ./results/ndm_md1.out -p ./results/ndm-wat.prmtop -c
>> > ./results/ndm_min2.rst -r ./results/ndm_md1.rst -x
>> ./results/ndm_md1.mdcrd
>> > -ref ./results/ndm_min2.rst
>> >
>> > Unit 30 Error on OPEN:
>> > ./results/ndm_md1.rst
>> > /var/spool/torque/mom_priv/jobs/5731.bircibm.SC: line 25:
>> > ./results/ndm_md2.rst: No such file or directory
>> > *
>> >
>>
>> I don't think you copied everything over correctly. Here it says that
>> ./results/ndm_md2.rst doesn't exist, but I don't see anywhere above where
>> you used that file.
>>
>>
>> > could anyone please give me a hint about this? I just dont understand
>> why
>> > it
>> > happened 'cause it ran fine for other molecules before. And why didnt it
>> > occur during minimization?
>> >
>> > Thank you very much, and really looking forward to your reply.
>> >
>> > Regards,
>> > Chinsu
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Tue May 17 2011 - 22:30:02 PDT
