[gmx-users] Error in using gromacs for MD simulation

Dallas Warren Dallas.Warren at monash.edu
Mon Apr 30 01:25:05 CEST 2012

I have posted this to the gromacs users emailing list.

No files came through, generally they are stripped off the emails before being posted to the emailing list.  Should never send attachments to an emailing list, post them to the internet and put the URLs in the email for people to look at if they want to.  People can't comment on what isn't available for them to see.

Can't suggest anything more about the error.  You simply have to find out why there is a difference between the number of atoms in the .gro file and the number defined by the .top file.  If you have checked your .gro and .top files, what did you find?  The fact that you still get a warning stating the numbers are different indicates you have still missed something.  And if you are following a tutorial, then you have done something different to what the tutorial has told you to do.  Incorrectly edited a file, used the wrong, old file in a new step etc.  Many ways you may have gone wrong.

Is it "1 SOL atom" or 1 SOL molecule?  Be very careful with your terminology with things like that, can seem the same to someone starting out, but they are very different.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: vineetha mandlik [mailto:vinee2here at gmail.com]
Sent: Saturday, 28 April 2012 5:30 AM
To: Dallas Warren
Subject: Regarding your reply in gromacs users forum

Respected Sir,

    I got your reference from the reply that you have given to the question I put up in Gromacs users forum. First of all I would like to thank you for your reply becos nobody seems to answer the question :) even though I had attached our output files too ... Sir there is problem running with our gromacs program. We carry out MD simulation of proteins using gromacs version 4.

And in that case the error obtained is number of coordinates in topology and coordinate file is not the same. As mentioned in gromacs tutorial we have edited even the SOL atoms in topology file, added required number of ions too...yet the same error repeats. We have cross checked both our top and gro files also.

Somehow we get a difference of 1 SOL atoms extra between the topology and coordinate file and we do not know how to proceed. I would like to ask you if you have any suggestions sir, any commands to vary...

Commands followed are from the following tutorial:


Thanking you.
Junior research fellow, India
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