[gmx-users] adding ETHANOL to CGennFF in gromacs has problem

[Justin Lemkul]

On 9/2/13 2:02 PM, Golshan Hejazi wrote:
> Thanks Justin for looking at the files. I am using the gro and top file to generate a tpr with the following mdp file in order to see if everything is all right:
>
> title                    = geometry-optimization
> cpp                      = /usr/bin/cpp
> include                  =
> integrator               = steep
> comm_mode                = Linear
> dt                       = 0.001
> nsteps                   = 1000000
> ; Output frequency for coords (x), velocities (v) and forces (f) =
> nstxout                  = 1000
> nstvout                  = 1000
> ; Output frequency for energies to log file and energy file =
> nstlog                   = 1000
> nstenergy                = 1000
> nstxtcout                = 1000
> xtc-precision            = 100000
> xtc_grps                 = System
> energygrps               = System
> pbc                      = xyz
> nstlist                  = 10
> epsilon_r                = 1.
> ns_type                  = grid ; or grid I don't know
> coulombtype              = pme
> vdwtype                  = Cut-off
> fourierspacing           = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order                = 4
> ewald_rtol               = 1e-05
> epsilon_surface          = 0
> optimize_fft             = yes
> rlist                    = 0.8
> rcoulomb                 = 0.8
> rvdw                     = 0.8
> emtol                    = 1.0
>

Note that your cutoffs are incorrect for strict adherence to CHARMM settings. 
See extensive threads from recent days and weeks on this topic.

> Yes, I am dealing with single molecule of ethanol. I can attach the tpr file and the resulting trr and gro file but it seems that the file size is big.

The mailing list does not accept attachments, nor are those files particularly 
informative (maybe the .gro, but that can easily just be pasted in an email for 
a single-molecule system).  Screenshots linked from some publicly accessible 
image-sharing site work well.

> When I visualize the trajectory. in the second step, the molecule is already without any bond ... it is separated atoms. I don't think this is visualization problem since I already tried all trjconv -pbc option.
>

Measurements of intramolecular distances are more informative than whether or 
not visualization software thinks there's actually a bond there.  The topology 
is definitive, visualization is not.  There may certainly be a problem, but be 
sure you're using quantitative assessments, not qualitative (and error-prone).

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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