Dear all,
I am having a problem in some of my simulations that only happens in pmemd.MPI. This is the error I get right before the simulation starts:
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
Coordinate resetting cannot be accomplished,
deviation is too large
iter_cnt, my_bond_idx, i and j are : 1 50 111 117
This error does not appear in pmemd, pmemd.cuda, pmemd.cuda.MPI, sander and sander.MPI, and the simulation finishes fine. This error happens both in the current amber from git and on Amber16. This error does not depend on the number of processors I choose.
After an inspection in the PMEMD code, I found out the error was being printed from shake.i :
! Shake resetting of coordinate is done here:
rrpr = zero
do m = 1, 3
rrpr = rrpr + xij(m) * xpij(m)
end do
if (rrpr .lt. toler * 1.0d-06) then ! Deviation too large. Kill PMEMD.
if (master) then
write(mdout, 321) iter_cnt, my_bond_idx, i, j
if (imin .eq. 1) write(mdout, 331)
end if
call mexit(6, 1)
end if
Here is where the 321 is defined:
321 format(/5x, 'Coordinate resetting cannot be accomplished,', &
/5x, 'deviation is too large', &
/5x, 'iter_cnt, my_bond_idx, i and j are :', 4i8)
I checked what values were being generated for the variables rrpr and toler for the atom pair 111 and 117 (for which the error happens on pmemd.MPI). For pmemd I get rrpr=0.9305 and toler=0.9216 and for pmemd.MPI I get rrpr=-28.1436 and toler=0.9216 . This negative value for rrpr is very strange (it should be positive by construction).
I am sending attached my parmtop and rst7 files so you may reproduce this error on your computers. Has anybody ever seen this problem before?
Best regards,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
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Received on Wed Jun 21 2017 - 11:30:02 PDT
