Hi all,
I have a protein-ligand system with 42000 atoms. I am running explicit solvent simulation. Every thing seems to be working fine except that the system has been crashed due to formatting error twice in the run. The error on the promopt looks like:
forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read
Image PC Routine Line Source
sander 082120F7 Unknown Unknown Unknown
sander 08211717 Unknown Unknown Unknown
sander 081D70F6 Unknown Unknown Unknown
sander 081A0338 Unknown Unknown Unknown
sander 0819FFD3 Unknown Unknown Unknown
sander 081AD9A2 Unknown Unknown Unknown
sander 081AC3BF Unknown Unknown Unknown
sander 080D3264 Unknown Unknown Unknown
sander 080D2F47 Unknown Unknown Unknown
sander 080A694C Unknown Unknown Unknown
sander 08073067 Unknown Unknown Unknown
sander 08072B69 Unknown Unknown Unknown
sander 08048265 Unknown Unknown Unknown
sander 0821CE98 Unknown Unknown Unknown
sander 08048131 Unknown Unknown Unknown
When the system crashed, it corrupted the rst file, which means I can not run the simulation again from the rst file generated by sander. I then, generated rst file with ptraj but sander didnot read the time point and the temperature and everything. I understand that rst is just the coordinate information but then I feel a huge difference in the rst file I use from sander and the one I use from ptraj. Do you recommend that I continue with the ptraj rst file. or should I start my simulation again from the previous rst that I had for my md run?
Secondly, the rst file that was corrupted in the middle of the run read something like this in the beginning:
<null><null><null><null><null><null><null><null><null><null><null><null><null><null><null><null><null>.......
-8.1563957 35.5523092 37.4035340 -7.6259480 34.6225382 36.3334237
.
.
.
.
.
...
Does anyone has any idea of what might be going wrong? Or its just a bad luck...
Thanks,
Regards,
Waqas.
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Received on Mon Dec 21 2009 - 04:00:02 PST
