[gmx-users] Sending an email, question

[Justin Lemkul]

On 3/26/15 3:27 PM, Poncho Arvayo Zatarain wrote:
>
>
>
> Hello, i´m new here and i have a question. I´m trying to replicate a DPPC128 membrane simulation of the Article Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do It of Martínez-Seara et al. This is mi mpd file and i´m using GROMACS 5.0.2
> Title: MD SIMULATIONintegrator : md dt : 0.002 (b) nsteps : 100000000  nstxout : 50000  nstvout : 50000  nstlog : 5000  nstenergy : 5000  nstxtcout : 5000  pbc : xyz  coulombtype : PME  rcoulomb : 1.0 rvdw : 1.4  tcoupl : Berendsen  tc-grps : System  tau_t : 0.1  ref_t : 325 Pcoupl : Berendsen  Pcoupltype : semiisotropic  tau_p : 2.0 2.0  compressibility : 4.5e-5 4.5e-5  ref_p : 1.0 1.0  constraints : all-bonds
> When i use grompp of the article:  grompp -f dppc128.mdp -c dppc.pdb -p topol_dppc.top -o dppc128_1.tpr (acoording to the names of my files) i got this error:
> Command line:  grompp -f dppc128.mdp -c dppc.pdb -p topol_dppc.top -o dppc128_1.tpr
>
> NOTE 1 [file dppc128.mdp, line 49]:  dppc128.mdp did not specify a value for the .mdp option "cutoff-scheme".  Probably it was first intended for use with GROMACS before 4.6. In 4.6,  the Verlet scheme was introduced, but the group scheme was still the  default. The default is now the Verlet scheme, so you will observe  different behaviour.
> Ignoring obsolete mdp entry 'title'Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
> ERROR 1 [file dppc128.mdp]:  With Verlet lists rcoulomb!=rvdw is not supported
>
> NOTE 2 [file dppc128.mdp]:  The Berendsen thermostat does not generate the correct kinetic energy  distribution. You might want to consider using the V-rescale thermostat.

The notes are there so you make better choices.  The error indicates that you're 
doing something that can't be done.

> Setting the LD random seed to 772888378
> -------------------------------------------------------Program grompp, VERSION 5.0.2Source code file: /root/GROMACS/gromacs-5.0.2/src/gromacs/gmxpreprocess/gmxcpp.c, line: 311
> Fatal error:Topology include file "dppc.itp" not foundFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors-------------------------------------------------------
>    		 	   		

So dppc.itp doesn't exist in the working directory, GMXLIB, or any additional 
location specified by the "include" keyword in the .mdp file.  It needs to be.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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