Hi,<br><br>The errpr msg. that I expressed in the previous mail is unclear.<br>It really happened in the grompp step of my dealinw with the em.<br>The manual shows that the viste can be used by <br><br>[ virtual sites2 ]<br>
; Site from funct a<br>5 1 2 1 0.7439756<br><br>What should I choose the vsite for the -CN group? (2, 3fd or others?)<br>I read the manual and the columns of the vsite need some parameters.<br>The "Site" seems to be the atom number.<br>
The "from" seems some atom group, but which atoms should be included?<br>How could obtain the "func" values?<br>Could you give me a molecule for my example?<br>Thanks for your help.<br><br>Best,<br><br>
Chia-yun<br><br><br><div class="gmail_quote">2011/2/19 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 text="#000000" bgcolor="#ffffff"><div class="im">
On 19/02/2011 3:02 PM, C.Y. Chang wrote:
</div><blockquote type="cite">Hi,<br>
<br><div class="im">
I have tried to add<br>
<br>
[ position restraints ]<br>
</div></blockquote>
<br>
This is misspelled. Surely grompp warned about this?<div class="im"><br>
<br>
<blockquote type="cite">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>
</blockquote>
<br></div>
This does not even approach the solution to your problem. Position
restraints inhibit diffusion and structural changes. You need a
vsite, like you knew earlier.<div class="im"><br>
<br>
<blockquote type="cite">In the em. process, I get the eroor msg.<br>
</blockquote>
<br></div>
No, this error happened in grompp.<div class="im"><br>
<br>
<blockquote type="cite">Fatal error:<br>
Invalid dihedral type 1000<br>
</blockquote>
<br></div>
GROMACS didn't recognise the mis-spelled directive, and so it's
trying to make sense of your position restraint lines as dihedrals.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite"> 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" target="_blank">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>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><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>
<br>
</div>
</div>
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