Hello,
It would be good if you may be able share your decharge input file and vdwaals removal input files.
That way people can comment if there is an issue with the input preparation.
Many thanks
Debarati
From: Delwakkada Liyanage, Senal Dinuka<mailto:sdd313.msstate.edu>
Sent: 10 January 2021 13:07
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: [AMBER] TI simulation blowing up with pmemd.CUDA
Dear Amber users,
I am trying to do TI in Amber18 with pmemd.cuda. The system is a small porphyrin ligand (
C44H38N8),
prepared in a 16 A TIP3P water box. When
using softcore potentials in the two-step transformation for removal of vdW interaction, the simulation crashes. I noticed that mdout resulted in excessive VDWAAL interaction energies.
TI region 1
NSTEP = 2997000 TIME(PS) = 243616.999 TEMP(K) =********* PRESS = 0.0
Etot = ************** EKtot = ************** EPtot = -22631739.3346
BOND = ************** ANGLE = -35.9490 DIHED = 0.0001
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = **************
EELEC = -28649.8232 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 84490.2572
Density = 1.0313
DV/DL = **************
------------------------------------------------------------------------------
Softcore part of the system: 90 atoms, TEMP(K) = 7735744996.28
SC_Etot= *********** SC_EKtot= *********** SC_EPtot = ***********
But when I do the calculation using pmemd.MPI (with 16 threads) with the same starting coordinates and velocities the calculation completes successfully.
It must be mentioned that before sampling, system is equilibrated for 6 ns at each lambda value, (16-point gaussian quadrature) and all simulations are started from the previous 'restart.'
I would really appreciate your thoughts on handling this setback.
Thank you
Senal Liyanage
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Received on Mon Jan 11 2021 - 07:30:02 PST
