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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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
;-)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">If you want to persist with what you have already done ……<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">What is the list of molecules under the [ molecules ] directive within the .top file?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">How many atoms are contained in each of those molecules?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Use that information to get the total number of atoms according to the topology, i.e. .top<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Re use on Windows, yes GROMACS can be installed on that OS, see the website for details on how to do that.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Medicinal Chemistry and Drug Action<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> vineetha mandlik [mailto:vinee2here@gmail.com]
<br>
<b>Sent:</b> Monday, 30 April 2012 10:58 PM<br>
<b>To:</b> Dallas Warren<br>
<b>Subject:</b> Re: [gmx-users] Error in using gromacs for MD simulation<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">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.
<br>
<br>
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
<br>
<br>
Thanks for your suggestions. <br>
<br>
Vineetha.<o:p></o:p></p>
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<p class="MsoNormal">On Mon, Apr 30, 2012 at 4:55 AM, Dallas Warren <<a href="mailto:Dallas.Warren@monash.edu" target="_blank">Dallas.Warren@monash.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I have posted this to the gromacs users emailing list.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">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.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Medicinal Chemistry and Drug Action</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Monash Institute of Pharmaceutical Sciences, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> vineetha mandlik [mailto:<a href="mailto:vinee2here@gmail.com" target="_blank">vinee2here@gmail.com</a>]
<br>
<b>Sent:</b> Saturday, 28 April 2012 5:30 AM<br>
<b>To:</b> Dallas Warren<br>
<b>Subject:</b> Regarding your reply in gromacs users forum</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt"><br>
Respected Sir,<br>
<br>
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.
<br>
<br>
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.<br>
<br>
<br>
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...<br>
<br>
Commands followed are from the following tutorial:<br>
<br>
<a href="http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf" target="_blank">http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf</a>.
<br>
<br>
<br>
<br>
Thanking you.<br>
Vineetha<br>
Junior research fellow, India<o:p></o:p></p>
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