Hi,<br><br>I have tried to add<br><br>[ position restraints ]<br>2 1 1000 1000 1000 ; Restrain to a point<br>1 1 1000 0 1000 ; Restrain to a line (Y-axis)<br>3 1 1000 0 0 ; Restrain to a plane (Y-Z-plane)<br><br>in the end of the topology file.<br>
<br>In the em. process, I get the eroor msg.<br><br>Fatal error:<br>Invalid dihedral type 1000<br><br><br> Chia-yun<br><br><br><div class="gmail_quote">2011/2/18 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><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">On 18/02/2011 1:13 PM, C.Y. Chang wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi,<br>
<br>
I am dealing with the lipid bilayer permeation simulation.<br>
Most compounds can be finished, but the compounds with CN can't be performed simulation.<br>
I have searched the discussion in the gmx-users discussion.<br>
The "vsite" has been mentioned, and I have refered to the gromacs manual.<br>
But I don't understand that how I can use the "vsite".<br>
</blockquote>
<br></div>
The theory is discussed in chapter 4 and there's a brief example in 5.2.2. What have you tried and what went wrong?<br>
<br>
Mark<div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
(add the toplogy file or use the command line?)<br>
I attach the PDB and toplogy file of the molecule.<br>
First, I performed the molecular dynamic simulation for the pure lipid bilayer, and the step was been finished.<br>
After I insert the molecule, these command lines are performed.<br>
<br>
grompp -f minim.mdp -c cmplx.pdb -p topol_dppc.top -o em.tpr<br>
mdrun -v -deffnm em<br>
grompp -f npt_cmplx.mdp -c em.gro -p topol_dppc.top -o npt_cmplx.tpr<br>
nohup mdrun -v -deffnm npt_cmplx &<br>
<br>
Thanks for your help.<br>
Best,<br>
<br>
Chia-yun<br>
</blockquote>
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