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

[Dallas Warren]

Please keep discussions on the emailing list so others at a later point can use the material if needed.  Unless of course you are paying me for my comments ;-)

What you really should do is go back to the start, fresh directory with nothing in it and start from the start.  Follow the steps provided in the tutorial you are following very closely.  You have obviously done something incorrect, since the tutorial works for many others.  Don't assume anything, skip steps or do it in a different manner to which it has told you.

If you want to persist with what you have already done ......

What is the list of molecules under the [ molecules ] directive within the .top file?

How many atoms are contained in each of those molecules?

Use that information to get the total number of atoms according to the topology, i.e. .top

Now open your .gro file using a text editor, second line of the file will be the number of atoms that the .gro file contains.

Compare the number from the .gro and the .top file.  You should find they are different, and that is what grompp has observed for you, hence the error you have gotten.

Now you have to go through and work out why there is a difference.  Only you can do that, no one else is going to do it for you.  Possible explanations include, but certainly not limited to; failure to update the number of molecules in the .top file after performing a step such as adding ions, deleting a coordinate line from the .gro file thereby removing a single atom, incorrect number of molecules entered into the .top file etc.

Another thing you can do is go through the .gro file, ensure that the number of molecules in the .top correspond to the number in the .gro file, and that for each molecule the atoms are the correct number.

Re use on Windows, yes GROMACS can be installed on that OS, see the website for details on how to do that.

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: Monday, 30 April 2012 10:58 PM
To: Dallas Warren
Subject: Re: [gmx-users] Error in using gromacs for MD simulation

And regarding the files I had manually jotted down all the aminoacids in top file and cross checked in gro file. Both the files do not show any mismatch. And it is a difference of coordinates in top file and gro file. The suggestion put up in gromacs website regarding this error doesnt seem to work. So either it is the machine creating the problem or as suggested by you some input file seems to be the culprit.

We do this in linux based platform. Can this be done on windows too? And ya u got it sir I am new to gromacs and the very first model fails ;)  ..anyways I will try to do it

Thanks for your suggestions.

Vineetha.
On Mon, Apr 30, 2012 at 4:55 AM, Dallas Warren <Dallas.Warren at monash.edu<mailto:Dallas.Warren at monash.edu>> wrote:
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<mailto: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<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:

http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf.



Thanking you.
Vineetha
Junior research fellow, India

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120501/0f8d612d/attachment.html>