[gmx-users] Implicit solvent simulation

[Eduardo Diniz]

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