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I am running a methanol simulation with a topology I obtained from Tinker for OPLS-AA, at 298 K and 1 bar. This is my .itp file:

[ atomtypes ] ; atm_kind symbol mass charge ptype sigma epsilon MTH0 C01 12.0110 0.000 A 0.35000 0.27614 MTH1 O02 15.9990 0.000 A 0.31200 0.71128 MTH2 H03 1.0080 0.000 A 0.25000 0.12552 MTH3 H04 1.0080 0.000 A 0.25000 0.12552 MTH4 H05 1.0080 0.000 A 0.25000 0.12552 MTH5 H06 1.0080 0.000 A 0.00000 0.00000 [ moleculetype ] ; residue nrexcl MTH 3 [ atoms ] ; srno atm_kind resnr res sym cgnr charge mass 1 MTH0 1 MTH C01 1 0.145 12.0110 2 MTH1 1 MTH O02 1 -0.683 15.9990 3 MTH2 1 MTH H03 1 0.040 1.0080 4 MTH3 1 MTH H04 1 0.040 1.0080 5 MTH4 1 MTH H05 1 0.040 1.0080 6 MTH5 1 MTH H06 1 0.418 1.0080 [ bonds ] ; p1 p2 funct r0 ks 1 2 1 0.1410 267776.000 1 3 1 0.1090 284512.000 1 4 1 0.1090 284512.000 1 5 1 0.1090 284512.000 2 6 1 0.0945 462750.400 [ angles ] ; p1 p2 p3 funct theta0 kb 2 1 3 1 109.500 292.880 2 1 4 1 109.500 292.880 2 1 5 1 109.500 292.880 3 1 4 1 107.800 276.144 3 1 5 1 107.800 276.144 4 1 5 1 107.800 276.144 1 2 6 1 108.500 460.240 [ dihedrals ] ; PROPER DIHEDRAL ANGLES ; p1 p2 p3 p4 funct c0 c1 c2 c3 c4 c5 3 1 2 6 3 0.736 2.209 0.000 -2.946 0.000 0.000 4 1 2 6 3 0.736 2.209 0.000 -2.946 0.000 0.000 5 1 2 6 3 0.736 2.209 0.000 -2.946 0.000 0.000

When I run the npt equilibration step before my production run, I get the following note:

NOTE 1 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance.

These are my constraints in my .mdp file:

continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; bonds involving H are constrained

Furthermore, my performance is pretty slow. I have 3000 methanol molecules, so 18000 atoms, and I am taking upwards of 24 hours to get 50 ns. What could be the cause of such a slow down? Methanol is a small, well-studied molecule and I want to benchmark TINKER before I move forward.

Any advice you have would be appreciated.

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    $\begingroup$ Did you try changing constraints to h-bonds? $\endgroup$ Commented Sep 19, 2021 at 6:27
  • $\begingroup$ What hardware are you running on? I once spent a couple days debugging performance on the "national flagship supercomputer" of a certain European country before I realized the performance issues were because the computer in question was old and due for replacement. (Also, I agree with @TristanMaxson that you should use h-bonds instead of all-bonds -- the comment in your mdp doesn't match the statement.) $\endgroup$ Commented Sep 19, 2021 at 7:19
  • $\begingroup$ yes, I will be trying changing to h-bonds. But my question is, what if i want to have all-bonds to be constrained? $\endgroup$ Commented Sep 19, 2021 at 23:41
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    $\begingroup$ ...Also, with 18000 atoms, that kind of speed doesn't sound unreasonable to me. It depends on how many processors you are running on. I don't remeber where I read this, but gromacs can become slow if the order of atoms in the [atoms] section is different. In my gromacs installation, the order of methanol atoms in OPLS-AA is different from the one you write, so maybe you can try using the default one and see if it makes the simulation faster? $\endgroup$ Commented Sep 20, 2021 at 13:25
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    $\begingroup$ Were any of the suggestions in the comments helpful? This gromacs page mentions that certain forcefields (including OPLS/aa) were parameterized with constrained h-bonds and shouldn't be used with all-atom constraints. $\endgroup$ Commented Oct 29, 2021 at 18:08

1 Answer 1

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After running some tests, the best way to overcome the slow performance was to simply use the constraints no h-bonds. There was no significant difference in densities and diffusion coefficient when constraint was changed to all-bonds.

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