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On 25/11/2011 6:53 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopy52hmPHyVUFNmVkZpnex9hEQ7NDzkruaaCKp93xvF9Hw@mail.gmail.com"
type="cite">This way I've already used but is this possible to
extract Gro and trp files from uncompleated runs and not stopping
this simulation ?<br>
</blockquote>
<br>
Copy the trajectory file. Then use trjconv on the copy however suits
you. You don't need a new .tpr, you need either the original .tpr or
one that suits your analysis.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopy52hmPHyVUFNmVkZpnex9hEQ7NDzkruaaCKp93xvF9Hw@mail.gmail.com"
type="cite"><br>
<br>
James<br>
<br>
<div class="gmail_quote">2011/11/25 Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#FFFFFF" text="#000000">
<div class="im"> On 25/11/2011 6:38 PM, James Starlight
wrote:
<blockquote type="cite">Mark, <span
style="color:rgb(121,6,25)">Tsjerk thanks!<br>
<br>
I've check my uncompleated produced MD run by G_energy
and find that average pressure is 1.1 Bar that is most
close to ref.<br>
<br>
<br>
By the way could you tell me about extra possible ways
of checking running simmulation? ( E.g I'm calculating
long produce trajectory and want to check my
uncompleated system ).<br>
<br>
As I understood One of the possible way is the ussage
of G_energy but how I could obtain GRO and TPR file
from uncompleated MD trajectory ( .trr) (recently I've
asked about this but I've missed that topic ;o) ?<br>
</span></blockquote>
<br>
</div>
Choose a length of time in advance that you are happy to
risk being wasted. Run that length of time, make a backup,
check whatever you want to check, then continue the
simulation. As you acquire confidence, you will want to
increase that time (and like everyone you will regret that
decision at least once!)<br>
<font color="#888888"> <br>
Mark</font>
<div>
<div class="h5"><br>
<br>
<blockquote type="cite"><span style="color:#790619"> <br>
<br>
<br>
Thanks again<br>
<br>
James<br>
</span><br>
<div class="gmail_quote">2011/11/25 Tsjerk Wassenaar <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:tsjerkw@gmail.com" target="_blank">tsjerkw@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<p>Hi James,</p>
<p>There have been extensive discussions about
this on the list. Check the archives. In short,
smaller systems give larger fluctuations, and
shorter simulations give larger deviations from
the expected average.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<font color="#888888"> </font>
<blockquote type="cite">
<div>
<div>On Nov 25, 2011 7:23 AM, "James
Starlight" <<a moz-do-not-send="true"
href="mailto:jmsstarlight@gmail.com"
target="_blank">jmsstarlight@gmail.com</a>>
wrote:<br>
<br>
Dear Gromacs Users!<br>
<br>
<br>
At the present time I'm simulating small
peptide (11 a.c in coiled conformation) in
water.<br>
<br>
I've desided to use parameters from Lysozyme
simmulation ( opls ff for parametrisation
and all mdp parameters from that
simulation).<br>
<br>
Because my peptide was smaller than typical
globular protein I've desided to use bigger
periodical box than in tutorial<br>
<br>
I've used editconf -c -d 1.5 -bt cubic
instead of 1.0 nm in tutorial wich resulted
in bigger box relative peptide size.<br>
<br>
so i have this box vectors 5.39318
5.39318 5.39318<br>
<br>
My experiment was in full agreement with the
above tutorial until NVP phase was
conducted. I have conducted 100ps
equilibration but When I've checked average
pressure it was 0.75 atm instead of 1 BAR
and have big RMSD- 200. (also I've checked
my system visually but it looks fine- I have
not pointed any artifacts linked with
unstable pressure like voids in the solvent
etc). Should I equilibrate my sustem longer
until pressure would not be stabilized to
reference BAR? What another options should
i take into account during simulation of the
small peptides ?<br>
<br>
Thanks,<br>
<br>
James<br>
<br>
</div>
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