- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Liao <liaojunzhuo.aliyun.com>

Date: Fri, 3 Apr 2020 18:42:58 -0500

Dear Amber users,

I’ve been running into a persistent problem that I have never really resolved. That when using the MMPBSA.py.MPI script for energy calculations, specifically the nmode entropy calculations part, it very easily gets stuck.

With drms=0.002, maxcyc=1000, I can see that in the nm.out file that gets stuck (usually stuck already by 200ns), the RMSG will go back and forth between a certain value, and never reach the drms value set. Whether maxcyc=1000 or 10000 doesn’t help, it usually gets stuck by iteration 200 or so.

If all frames are good, they finish in an hour or so. When a single frame has this problem, after a few hours, it finishes with an error, but it still saves a result file, minus one (stuck) entropy frame. But there are times when more than one frame is stuck and nothing gets saved after a few hours.

Have others been also getting this problem, frequently? If so, is it the structure problem, or a calculation set up problem?

Many thanks.

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Fri Apr 03 2020 - 17:00:01 PDT

Date: Fri, 3 Apr 2020 18:42:58 -0500

Dear Amber users,

I’ve been running into a persistent problem that I have never really resolved. That when using the MMPBSA.py.MPI script for energy calculations, specifically the nmode entropy calculations part, it very easily gets stuck.

With drms=0.002, maxcyc=1000, I can see that in the nm.out file that gets stuck (usually stuck already by 200ns), the RMSG will go back and forth between a certain value, and never reach the drms value set. Whether maxcyc=1000 or 10000 doesn’t help, it usually gets stuck by iteration 200 or so.

If all frames are good, they finish in an hour or so. When a single frame has this problem, after a few hours, it finishes with an error, but it still saves a result file, minus one (stuck) entropy frame. But there are times when more than one frame is stuck and nothing gets saved after a few hours.

Have others been also getting this problem, frequently? If so, is it the structure problem, or a calculation set up problem?

Many thanks.

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Fri Apr 03 2020 - 17:00:01 PDT

Custom Search