[gmx-users] Implicit solvent simulation

[Mark Abraham]

Hi,

The implicit solvation implementation was broken with multiple threads for
quite a few years, I'm afraid. So we have removed it for the upcoming 2019
release. I strongly recommend running it with only one thread (so use
-ntmpi 1), or use the version in GROMACS 4.5.7 if you need the performance.

Mark

On Fri, Oct 26, 2018 at 5:21 PM Eduardo Diniz <dududiniz94 at hotmail.com>
wrote:

> Hello dear users!
>
> I'm trying to set up an implicit solvent simulation of a protein in
> gromacs, but I haven't found much about the details of how to do it. After
> generating topology: gmx pdb2gmx -f protein.pdb  (I selected the amber99sb
> forcefield and none for water)
> I've done an energy minimization using the same mdp file I use for
> explicit solvent minimizations:
>       gmx grompp -f em.mdp -c conf.gro -p topol.top -o em.tpr
>       gmx mdrun -deffnm em -v
> Everything went well. Then, started the simulation part. For this I found
> a mdp file in http://www.strodel.info/index_files/lecture/md-implicit.mdp
> and used it the way it was, only changing the ns_type option from simple to
> grid and the step size dt form 0.005 to 0.0005
> www.strodel.info<
> http://www.strodel.info/index_files/lecture/md-implicit.mdp>
> integrator = md dt = 0.005 ; ps ! nsteps = 20000000 ; total 1 ns. nstxout
> = 100 nstvout = 100 nstfout = 100 nstlist = 10 nstlog = 100 cutoff-scheme =
> group rlist = 5 rvdw = 5 rcoulomb = 5 coulombtype = cut-off vdwtype =
> cut-off bd_fric = 0 ld_seed = -1 pbc = no ns_type = simple constraints =
> all-bonds lincs_order = 4 lincs_iter = 1 lincs-warnangle = 30 Tcoupl =
> v-rescale tau_t = 1.0 tc-grps ...
> www.strodel.info
>
> When I ran:
>    gmx mdrun -deffnm md -v
> I've got a long list of errors:
>
> Reading file md.tpr, VERSION 5.1.4 (single precision)
> Using 8 MPI threads
>
>
> NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
> removed in a future release when 'verlet' supports all interaction forms.
>
> WARNING: This run will generate roughly 12519 Mb of data
>
>
> Increasing the number of cell to communicate in dimension X to 3 for the
> first time
>
> Increasing the number of cell to communicate in dimension Y to 2 for the
> first time
>
> Increasing the number of cell to communicate in dimension Z to 2 for the
> first time
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.069491, max 1.607370 (between atoms 5502 and 5503)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.016753, max 0.691331 (between atoms 5538 and 5540)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 5.382844, max 48.498402 (between atoms 3573 and 3575)
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 1.628109, max 34.554295 (between atoms 7226 and 7227)
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.232295, max 5.191326 (between atoms 5538 and 5539)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 3.202004, max 55.350895 (between atoms 7228 and 7230)
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 2.597767, max 43.021877 (between atoms 7241 and 7242)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.402189, max 8.099020 (between atoms 5502 and 5505)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.165958, max 3.489924 (between atoms 5544 and 5546)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.076343, max 3.150469 (between atoms 5538 and 5540)
>
> And more of this shows up till it ends with segmentation fault. Even not
> using lincs, the lincs warning keep appearing. I'm using gromacs version
> 5.1.4
>
> I would appreciate if anyone could help me figure out how to solve this.
>
> Eduardo
>
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