Dear AMBER users,
I have been using PMEMD-CUDA during the past few months to perform MD umbrella sampling simulations to obtain the free energy profile of a small molecule (HgBr2) going through an air-water interface. I have followed an approach similar to the one presented on the AMBER tutorial 7.5 (Transferring methanol trough a membrane), which for my specific case requires the definition of a distance restraint between the center of mass of HgBr2 and the center of mass of the 1499 water molecules that define my water layer.
Now I am planning on obtaining this free energy profile at the QM-MM level using sander, but I have encountered with the 200 atoms limitation in the group definition of the distance restraint file. I read in the manual that this limitation is not present in PMEMD, which is why I was able to define a group of 4500 atoms (all O and H atoms of the 1499 water molecules).
Nevertheless, I have tried to carry out a simulation with sander using this distance restraint file:
&rst
iat=-1,-1,
r1=-10.00,
r2=0.00,
r3=0.00,
r4=10.00,
rk2=10.0,
rk3=10.0,
iresid=0,
fxyz=0,0,1,
outxyz=1,
igr1=1,2,3,
igr2=4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,/
which has 201 atoms on the second group definition and, because of that, it obviously stops. However, it gives the following error:
Error: Too many atom ranges need to be stored for center-of-mass distance
restraints. MAXGRP = 1. This needs to be increased.
Because of that, I wanted to ask if it was possible to get rid of the 200 atoms limitation in sander by increasing this variable (which by reading earlier posts from the forum I think it would require to modify the code and recompile). I am unsure though about how this can be done and if this modification can affect negatively other parts of the code. Another possibility could be to reduce my system (and maybe only use the oxygen atoms of the water molecules for the group definition, allowing me to at least have 200 water molecules), but I am interested in exploring first this modification.
Thank you beforehand and best regards,
Javier Carmona García
Institute of Molecular Science (ICMol)
Valencia, Spain
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Received on Wed Jan 11 2023 - 07:00:02 PST
