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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Are you running constant pressure? If so, not surprising the box is shrinking, since it is a vacuum. You should use constant volume.<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">Also, you cannot change the values of those settings you have within the .mdp unless you have a good reason to and/or it is allowable by the forcefield. These
have particular values as defined by the forcefield, and you need to use those.<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"><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>
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<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""> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>On Behalf Of </b>Anik Sen<br>
<b>Sent:</b> Monday, 7 May 2012 2:55 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] Cut off problem<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Dear Gromacs users,<br>
<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="color:black">I am using GROMACS 3.3.2. I have a problem in setting the cut off of my MD-run.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="color:black">I want to see the interaction between some small atoms keeping them inside a periodic box without adding any solvent; i.e interaction between the atoms in the vacuum.
<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="color:black">I have a total of 18-25 atoms in my system. The initial minimization was ok, but in case of the MD run, the job is failing after a few steps with the error,<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<b><span style="color:black">Fatal error:</span></b><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<b><span style="color:black">"One of the box vectors has become shorter than twice the cut off length or one of the box diagonal element has become smaller than cut off".</span></b><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="color:black">I have already changed the ‘d’ and ‘rlist’; rvdw’ and rcoulomb’ to a number of different values to overcome the problem, but the problem persists.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="color:black">How can I overcome this problem.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="color:black">Thanking you in advance<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="color:black">Anik Sen<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif"">========================================================<br>
Anik Sen<br>
Student<br>
CSIR-Central Salt & Marine Chemicals Research Institute,<br>
Gijubhai Badheka Marg.<br>
Bhavnagar, Gujarat 364002<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";border:solid windowtext 1.0pt;padding:0cm"><img id="_x0000_i1025" src="cid:~WRD000.jpg" alt="Image removed by sender. www.csmcri.org"></span><span style="font-size:9.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif"">========================================================<o:p></o:p></span></p>
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