Thanks Tsjerk<br>
I referred the mail about the broken molecules but
there the problem is i think somewhat different. in that case broken
molecules are coming becasue of the PBC . since PBC is being used that
is why some part of the molecule is coming from the other side of box
and its looking as if protein is broken <br>
<br>
but in my case i think the situation is different, first of all i have
not still started using the PBC in the simulation and my full molecule
(broken molecule) is right in the center of the box. moreover i
am getting this problem before starting any simulation. till i did some
simulation in vaccum before adding ions , it went fine there and then
while shifting to the water simulation i added ions and right after
adding the ions my molecule is getting broken.<br>
<br>
<br>
Thanks <br>
With Regards <br>
Gurpreet<br>
<br>
7/16/07, <b class="gmail_sendername">Tsjerk Wassenaar</b> <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:<div><span class="gmail_quote"></span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Gurpreet,<br><br>I didn't ask whether you used PBC, I suggested it was due to PBC.<br>Check the archives for "broken molecules" and such.<br><br>Tsjerk<br><br>On 7/16/07, gurpreet singh <<a href="mailto:gps.iitm@gmail.com">
gps.iitm@gmail.com</a>> wrote:<br>> Thanks Tsjerk for you reply<br>> i did not get your point . i think you are asking me whether i used PBC or<br>> not , so i want to tell you that the .tpr file which i used for genion
<br>> command was created without using PBC.<br>><br>> but will it make any difference ?<br>><br>> Thanks<br>> With Regards<br>> Gurpreet<br>><br>> On 7/16/07, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">
tsjerkw@gmail.com</a> > wrote:<br>> ><br>> > Gurpreet,<br>> ><br>> > > my system was going fine at that time but when i used the genion<br>> command to<br>> > > add ions , i found that my protein was broken into parts.
<br>> > > what could be the reason for this ?<br>> ><br>> > PBC?<br>> ><br>> > > While running the genion it usually asked for the group into which we<br>> want<br>> > > to add the ions so i have checked with both the SOL group and OTH group
<br>> > > seperatly , in both the cases ions were replacing the solvent molecules.<br>> Is<br>> > > their any way by which we can add ions without replacing any solvent<br>> > > molecules ?<br>
> ><br>> > No, there's no space to put them.<br>> > Well, you could try to squeeze them in here or there manually, and<br>> > perform energy minimization...<br>> ><br>> > Cheers,<br>
> ><br>> > Tsjerk<br>> ><br>> ><br>> > --<br>> > Tsjerk A. Wassenaar, Ph.D.<br>> > Junior UD (post-doc)<br>> > Biomolecular NMR, Bijvoet Center<br>> > Utrecht University
<br>> > Padualaan 8<br>> > 3584 CH Utrecht<br>> > The Netherlands<br>> > P: +31-30-2539931<br>> > F: +31-30-2537623<br>> > _______________________________________________<br>> > gmx-users mailing list
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</a><br>><br><br><br>--<br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8<br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931<br>F: +31-30-2537623
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