[gmx-users] Error while performing a REMD simulation

Justin A. Lemkul jalemkul at vt.edu
Sun Apr 10 03:23:47 CEST 2011

Luis Miguel Medina Solano wrote:
> Hello,
> I'm very sorry for the way I reply, the truth is that i didn't know how 
> else to reply (it is my first time posting here).
> the script to generate the REMD is:
> #!/bin/bash
> # ff opsla and water spc
> #
> echo -e "14\n4\n3\n3 0" |pdb2gmx -f 1.pdb -o inib4em.pdb -p topol.top 
> -ignh -ter
> editconf -f inib4em.pdb -o inib4em.pdb -d 0.34 -bt dodecahedron

Using a solute-box distance of only 0.34 nm is probably unwise.  Why have you 
chosen such a short distance?

> grompp -v -f iniem.mdp -o em -c inib4em.pdb -maxwarn 5

Why are you using -maxwarn, especially to ignore up to five errors?  The notes 
that grompp prints are helpful in that they usually indicate sources of 
instability in your system by way of algorithm conflict.

> mdrun -v -s em -c ini_after_em.pdb -deffnm ini_after_em   
> editconf -f ini_after_em.pdb -o ini_after_em.pdb -d 0.34 -bt dodecahedron
> genbox  -cp ini_after_em.pdb -cs spc216 -o sol_b4em.pdb -p topol.top
> grompp -v -f em.mdp -c sol_b4em.pdb -o sol_em -p topol.top -maxwarn 5
> mdrun -v -s sol_em -c sol_after_em.pdb -deffnm sol_after_em
> grompp -v -f rp.mdp -c sol_after_em.pdb -o sol_rp -p topol.top -maxwarn 5
> mdrun -v -s sol_rp -c sol_after_rp.pdb -deffnm sol_after_rp
> # NVT and NPT runs for each replica
> for ((i = 0; i<= 42 ; i ++))
> do
> grompp -v -f nvt$i.mdp -c sol_after_rp.pdb -o sol_nvt$i -p topol.top 
> -maxwarn 5
> mdrun -v -s sol_nvt$i.tpr -c sol_after_nvt$i.pdb -deffnm sol_after_nvt$i
> grompp -v -f npt$i.mdp -c sol_after_nvt$i.pdb -o sol_npt$i -p topol.top 
> -maxwarn 5
> mdrun -v -s sol_npt$i.tpr -c sol_after_npt$i.pdb -deffnm sol_after_npt$i
> editconf -f sol_after_npt$i.pdb -o sol_after_nptt$i.pdb  -c
> grompp -v -f solv$i.mdp -c sol_after_nptt$i.pdb -o sol_solv$i -p 
> topol.top -maxwarn 5

Providing your .mdp files is probably useful for determining the source of your 
problems, but more likely either (or both) of the above points will have 
critical clues.


> done
> # REMD run
> mpiexec -l -np 43 mdrun_mpi -v -s sol_solv.tpr -multi 43 -replex 500 -c 
> Folded.pdb -deffnm Folded
> Best regards


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list