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GROMACS Issues

CANNOT RUN MD SIMULATION

Dear Sir,
 
Good Morning, Greetings From Portugal.
 
I am J. Muthukumaran working as a Post-doctoral Research Fellow in New University of Lisbon, Portugal. I am trying to run Gromacs MD simulation using web server, But I could not able to get the results page, it shows error. For your kind information, herewith I attached the screen shot of error message. And I am forwarding the uname and pwd mail.
 
Please kindly fix this.
 
Thanks in advance
Issue status: 
Open

fatal error

Fatal error:

number of coordinates in coordinate file (gmx-316563-sol.gro, 6893)

             does not match topology (gmx-316563-sol.top, 9034)

Issue status: 
Closed

Number of .xtc and/or .edr files does not match number of partitions

I am getting error "Number of .xtc and/or .edr files does not match number of partitions thus files are missing".

Kindly help.

Issue status: 
Open

My login or password are not recognized

As in the title, I cannot access the service through my accoutn. My username or password are not recognized and even by turnin gto http://www.wenmr.eu/wenmr/getting-started-gromacs nothing hppens. I must have done something wrong, but I cannot go about it. Any suggestions?

 

Thanks in advance

 

 

Mario A Pagano

 

Issue status: 
Closed

can not start a simulation

I tries to start a simulation with a binary input file so i placed tpr and cpt files in upload form, i submitted run but i encountered this error:

A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurre

and at the bottom of error page this error is seen:

Issue status: 
Open

GROMACS Too many LINCS warnings (1032)

Hi

I submitted my job as a PDB file but after analysing my job failed and the reason is "Too many LINCS warnings (1032)". 

Issue status: 
Closed

PROXY ERROR

Hi,

       I have submitted the pdb file for MD simulation by GROMACS, But after one or two days i get the mail about the failure of my submission. I have repeated it many times but always i get the error. When i check the log file for the error issue, I have found something like as follows:

 

GRM ERROR  835214-1: Cannot retrieve job status, reason:       user retrieved output sandbox destination:         khaldun.biruni.upm.my:8443/cream-pbs-academicgrid
Issue status: 
Closed

pdb file of enzymes are not read by GROMACS webportal

hello

My enzyme pdb files are never took by the GROMACS web portal.

always the error msg comes-

This occurange is logged. For more information, please send an email to m.vandijk1@uu.nl.
Our appologies for being unable to process your request. With kind regards, the GROMACS server team.

ERROR: The following residue codes are not regonized by the GROMACS topology generation procedure: 527. Stopping

 

Issue status: 
Closed

unable to run gromacs for my pdb

when i am tried to run gromacs for my pdb file the following problm shows as Unknown username: apoorv or password. If you have a WeNMR VRC account, did you subscribe to the GROMACS web portal? For more information visit: http://www.wenmr.eu/wenmr/getting-started-gromacs.

while my user name is apoorv

Issue status: 
Closed

MARTINI force field in GROMACS web server?

 

Hi,

I understand that the GROMACS web server has only recently been setup and running... but any ideas on including the MARTINI ff and some CG bilayer systems online?

Issue status: 
Closed

Cite WeNMR/WestLife

 
Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
 
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
 
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

EGI-approved

The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858

West-Life