<div>By the way, for the optimal setup of molecluar dynamics, there are some difference for gromacs and gromos, such as in the mdp file, GROMOS 96 force field uses nstlist = 5 and rvdw = 1.4.</div>
<div>Can anyone give me a standard mdp file to do MD simulation with gromacs package using gromos96 force field?</div>
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<div>Great thanks<br><br> </div>
<div><span class="gmail_quote">On 3/21/06, <b class="gmail_sendername">Shulin Zhuang</b> <<a href="mailto:shulin.zhuang@gmail.com">shulin.zhuang@gmail.com</a>> wrote:</span>
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<div>Dear All,</div>
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<div>I use gromacs version 3.3 to perform a simulation on a protein-drug complex. I chose the gromos96 53a6 force field. But how to generate the parameter file of the drug fo gromos96 53a6 force field. The Dundee PRODRG server produce files in format of gromacs/gromos87.
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<div>But the produce files of drugs such as itp file is not full agreement with gromos96 format. For example, in the itp file of the drug, as far as the bonds are concered, in gromacs, the funct is set to 1,while in gromos96 ,it is 2. Should I just change the funct value to 2 to keep it in agreement with gromos96 force field? For the atom type, I can edit them. But the bonds parameter is difficult for me to convert them to gromos96 force field. Would anyone give me any suggestion?
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<div>best regards<br clear="all"><br>-- <br> Shulin Zhuang<br>Chemistry Department <br>Zhejiang University PRC<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:shulin.zhuang@gmail.com" target="_blank">
shulin.zhuang@gmail.com</a> </div></div></blockquote></div><br><br clear="all"><br>-- <br> Shulin Zhuang<br>Chemistry Department <br>Zhejiang University PRC<br><a href="mailto:shulin.zhuang@gmail.com">shulin.zhuang@gmail.com
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