FW: [gmx-users] charmm and oplsaa simulation results don't match

Berk Hess gmx3 at hotmail.com
Tue Aug 19 15:42:41 CEST 2008

From: gmx3 at hotmail.com
To: sarbani_c84 at rediffmail.com
Subject: RE: [gmx-users] charmm and oplsaa simulation results don't match
Date: Tue, 19 Aug 2008 10:47:02 +0200


There are two main issues here.

One is sampling. I don't know what the correlations times in your systems are.
You say you obtain a few microstates. But does the system revisit the same
microstates over the 100 ns? If not, your simulations are certainly too short
to have full sampling and you can not expect that two simulations with the same
or different force fields produce the same sampling.

The second issue is the force field. Different force fields can favor different
configurations. This is especially true for backbone dihedrals. This will have
stronger effects on small peptides than on larger (less flexible) proteins.

And finally, it seems you are running with a plain Coulomb cut-off.
This will produce artefacts. You should use PME (or at least a reaction-field).


Date: Tue, 19 Aug 2008 08:28:25 +0000
From: sarbani_c84 at rediffmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] charmm and oplsaa simulation results don't match


Hi everybody,

                    I had run a long 100ns simulation on a tripeptide using opls/aa force field and 

spc water model.

I got a few microstates.

Then I tried to run simulation on the same system using charmm force field and tip3p water 


However I couldn't find the microstates. Within the first 10 ns the system adopts the final

 configuration that was observed in the simulation using oplsaa force field.



 The process I used to run gromacs with charmm and tip3p water model is


 pdb2gmx -f opls.gro -ff charmm -ter -water tip3p


 charmm27-run-addtop-gromacs-dihe.sh topol.top new.top



 mv new.top topol.top



 #### I did modify the top file to include "tip3p-charmm.itp" 

 for water topology.



 editconf -f conf.gro -o box.gro -bt cubic -d 0.75


 genbox -cs spc216.gro -cp box.gro -p topol.top -o solvated.gro


 grompp -zero -f em.mdp -c solvated.gro -o em.tpr



 mdrun -v -s em.tpr



 Then I generated the "tpr" file for 100ns.


 The em.mdp file includes :




;       User spoel (236)

;       Wed Nov  3 17:12:44 1993

;       Input file


cpp                 = /usr/bin/cpp

constraints         =  none

integrator          =  steep

nsteps              =  100


;       Energy minimizing stuff


emtol               =  2000

emstep              =  0.01

nstcomm             =  1

ns_type             =  grid

rlist               =  1

rcoulomb            =  1.0

rvdw                =  1.0

Tcoupl              =  no

Pcoupl              =  no

gen_vel             =  no

The 100ns.mdp file includes:


;       User spoel (236)

;       Wed Nov  3 17:12:44 1993

;       Input file


title               =  Yo

cpp                 =  /usr/bin/cpp

constraints         =  all-bonds

integrator          =  md

dt                  =  0.002    ; ps !

nsteps              =  50000000 ; total 10000 ps.

nstcomm             =  1

nstxout             =  250

nstvout             =  1000

nstfout             =  0

nstlog              =  250

nstenergy           =  250

nstlist             =  10

ns_type             =  grid

rlist               =  1.0

rcoulomb            =  1.0

rvdw                =  1.0

; Berendsen temperature coupling is on in two groups

Tcoupl              =  berendsen

tc-grps             =  Protein  SOL

tau_t               =  0.1      0.1

ref_t               =  300      300

; Energy monitoring

energygrps          =  Protein  SOL

; Isotropic pressure coupling is now on

Pcoupl              =  berendsen

Pcoupltype          = isotropic

tau_p               =  0.5

compressibility     =  4.5e-5

ref_p               =  1.0

; Generate velocites is off at 300 K.

gen_vel             =  no

gen_temp            =  300.0

gen_seed            =  173529

Can anyone suggest why am I not getting the microstates with "charmm " force field.

Is there anything more that I needed to do and I missed. I am sorry for such a lengthy query

Thanks in advance


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