[gmx-users] Re: A note while running grompp for nvt equilibration

[Justin Lemkul]

On 2/19/13 1:36 AM, Anu Chandran wrote:
> Sir,
> Thank you for the reply. As per the suggestion, I tried increasing the
> rlist. Note or warning stopped when rlist was increased to 1.8. Also with
> this value of rcoulomb, the box size also needs to be increased. I would
> like to know whether it is fine to keep rlist 1.8 and also whether there is
> any other alternative rather than increasing rlist since increase in rlist
> requires an increase in box size.

I would investigate why you have such large charge groups.  For a protein in 
water (which is what you appear to have based on the .mdp file), you should not 
have such large charge groups.  Haphazardly adjusting cutoffs can have a 
negative effect on the simulation.  Increasing rlist may result in poorer 
performance.  Why are you using a switching potential for van der Waals 
interactions?  Exact specifications for OPLS are hard to come by in the 
literature, but most commonly one sees:

rvdw = 1.0
vdwtype = cutoff
rlist = 1.0
rcoulomb = 1.0
coulombtype = PME

-Justin

> Thank you,
> with regards
> Anu
>
> On Fri, Feb 15, 2013 at 5:28 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:
>
>>> I am tyring to do a simulation of a monomer and an octamer of the same
>>> molecule
>>> using gromacs 4.5.3 with opls force field. Monomer simulations ran with
>> out
>>> any note or
>>> warning, but when i tried to do nvt equilibration for the octamer, i got
>> the
>>> following note while running grompp
>>>
>>> "NOTE 1 [file nvt.mdp]:
>>>    The sum of the two largest charge group radii (0.779095) is larger than
>>>    rlist (1.400000) - rvdw (1.000000)"
>>> The mdp file used is as follows:
>>>
>>> define                  = -DPOSRES
>>> integrator              = md
>>> dt                      = 0.002
>>> nsteps                  = 50000
>>> nstcomm                 = 10
>>> nstxout                 = 100
>>> nstvout                 = 100
>>> nstlog                  = 100
>>> nstenergy               = 100
>>> nstlist                 = 5
>>> ns_type                 = grid
>>> pbc                     = xyz
>>> rlist                   = 1.4
>>> coulombtype             = PME
>>> rcoulomb                = 1.4
>>> epsilon_r               = 1
>>> vdwtype                 = Switch
>>> rvdw_switch             = 0.9
>>> rvdw                    = 1.00
>>> fourierspacing          = 0.12
>>> pme_order               = 4
>>> ewald_rtol              = 1e-5
>>> optimize_fft            = yes
>>> Tcoupl                  = nose_hoover
>>> tc_grps                 = Protein  Non-Protein
>>> tau_t                   = 0.4      0.4
>>> ref_t                   = 300      300
>>> nh-chain-length         = 1
>>> pcoupl                  = no
>>> gen_vel                 = yes
>>> gen_temp                = 300.0
>>> gen_seed                = 1984
>>> continuation             = no
>>> constraints              = all-bonds
>>> constraint-algorithm     = LINCS
>>> lincs-order              = 4
>>> lincs-iter               = 1
>>> lincs-warnangle          = 30
>>>
>>>
>>> Can anybody please help me on how to go about with it?
>>
>>
>> 1) Increase RLIST
>> 2) Re-distribute atoms among charge groups so that to make charge
>> groups [spatially] smaller.
>>
>>
>>
>> Dr. Vitaly V. Chaban
>> MEMPHYS - Center for Biomembrane Physics
>> Department of Physics, Chemistry and Pharmacy
>> University of Southern Denmark
>> Campusvej 55, 5230 Odense M, Denmark
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================