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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Dear Gromacs users,<br>
<p class="MsoNormal" style="text-align:justify"><span style="font-size:12pt; line-height:115%; font-family:"Times New Roman","serif"">I am using GROMACS 3.3.2. I have a problem in setting the cut off of my MD-run.</span></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-size:12pt; line-height:115%; font-family:"Times New Roman","serif"">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. </span></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-size:12pt; line-height:115%; font-family:"Times New Roman","serif"">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,</span></p>
<p class="MsoNormal" style="text-align:justify"><b style=""><span style="font-size:12pt; line-height:115%; font-family:"Times New Roman","serif"">Fatal error:</span></b></p>
<p class="MsoNormal" style="text-align:justify"><b style=""><span style="font-size:12pt; line-height:115%; font-family:"Times New Roman","serif"">"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></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-size:12pt; line-height:115%; font-family:"Times New Roman","serif"">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.</span></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-size:12pt; line-height:115%; font-family:"Times New Roman","serif"">How can I overcome this problem.</span></p>
<p class="MsoNormal" style="text-align:justify"><br>
<span style="font-size:12pt; line-height:115%; font-family:"Times New Roman","serif""></span></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-size:12pt; line-height:115%; font-family:"Times New Roman","serif"">Thanking you in advance</span></p>
<p class="MsoNormal" style="text-align:justify"><span style="font-size:12pt; line-height:115%; font-family:"Times New Roman","serif"">Anik Sen<br>
</span></p>
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<div style="font-size:9pt; 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<br>
<div><img alt="www.csmcri.org" src="http://www.csmcri.org/images/logo.png"></div>
========================================================</div>
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