Hi Mark<br><br>I saw both the .gro file of hexane before and after EM in VMD as well checked their coordinates. I am not able to make anything out of it. it will better if one knows how to find the steric clash between two molecules?.<br>
<br>Regards<br>Vinoth <br><br><div class="gmail_quote">On Wed, Oct 6, 2010 at 11:08 AM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im"><br><br>----- Original Message -----<br>From: vinothkumar mohanakrishnan <<a href="mailto:kmvinoth@gmail.com" target="_blank">kmvinoth@gmail.com</a>><br>Date: Wednesday, October 6, 2010 15:20<br>Subject: [gmx-users] Reg: Energy minimisation of hexane<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Hi all<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I am trying to simulate 150 molecules of hexane in a triclinic box (8.319*3.01*3.01 nm^3) using OPLSAA force field.I got the .gro file from PRODRG and generated the topology using X2top command. when i run energy minimisation for hexane my potential energy is positve. is this right?. what i should correct to get the potential energy as negative. below is my result. any help is highly appreciated.<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Steepest Descents converged to Fmax < 100 in 10454 steps<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Potential Energy = 3.4133051e+04<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Maximum force = 9.8812309e+01 on atom 635<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Norm of force = 7.9230022e+00<br><br></div>So something is unhappy, and the minimizer can't deal with it. Probably you have some massive steric clash, like two molecules overlying each other. Look at the contents of your simulation cell before and after EM.<br>
<br>Mark<div class="im"><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;"> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Below is my contents of my em.mdp file<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>integrator = cg <br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>emtol = 100.0 <br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>emstep = 0.01 <br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>nsteps = 50000 <br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>nstcgsteep = 1000<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>nstlist = 1 <br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>ns_type = grid <br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font> rlist = 1.0 <br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>coulombtype = PME <br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>fourierspacing = 0.12<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>rcoulomb = 1.0 <br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>rvdw = 1.0 <br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>pbc = xyz <br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Regards<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Vinoth <br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br>
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