Hi
I am trying to do a simple TI (disappearing of a cation in a water box) with Amber12 sander using softcore potential. I have a couple of confusions:
1- The A9 tutorial sets up different crgmask values for V0 and V1 processes, thus making different mdin files and also different starting coordinates, leading to a group file like this (from the liked shell script):
-O -i mdin_min_v0_l${X} -o ${pre0}_min_v0_l${X}.out -p ${pre0}.prm -c ${pre0}.rst -r ${pre0}_min_v0_l${X}.rst
-O -i mdin_min_v1_l${X} -o ${pre1}_min_v1_l${X}.out -p ${pre1}.prm -c ${pre1}.rst -r ${pre1}_min_v1_l${X}.rst
But under the related topic, page 114 of the manual clearly says: "The input (mdin) and starting coordinate files must be the same for the two groups". Also when I use different mdin and/or starting coordinate files, sander.MPI crashes with the following last lines in the output:
| MPI Timing options:
| profile_mpi = 0
As I understand (implied by the tutorial), we should somewhere specify the atoms that are changing in the prmtop and it is implied that crgmask (or scmask?) does this. So it makes sense more to me that the mdin files should be different. But it doesn't work this way. Can someone explain why the manual and tutorial are different and which is the correct way?
2- It is implied from page 113 of the manual that an important difference between the new softcore potential TI method with the old one is that we don't need the dummy atom and so the number of the atoms in the prmtop can be different. It says: "This will remove the requirement to prepare "dummy" atoms and allows the two prmtop files to have different numbers of atoms." However, in page 114, it says: "Furthermore,
the two prmtop files must have the same number number of atoms, in the same order (since one
common set of coordinates will be used for both.)" So this is also confusing. Does the second statement refer to the old method? Or ...?
Thank you for your kind help.
Hamed S. Hayatshahi
Graduate Student of Medicinal Chemistry
University of Utah
+1 (801) 807 4121
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Received on Fri Aug 30 2013 - 11:30:02 PDT
