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Thanks so much for the answer.<br>
I have one more doubt. Could you please answer?<br>
I could make the change and run, but still the following line in the
log file, "Starting time for run is 0 ps" (BLUE color), appears
controversial to me. <br>
The log message is as follows.<br>
######################################################<br>
<font color="#ff0000">Checking consistency between energy and charge
groups...<br>
getting data from old trajectory ...<br>
Reading Coordinates, Velocities and Box size from old trajectory<br>
Will read till time 20000<br>
trn version: GMX_trn_file<br>
Reading frame 60 time 19917.312 Using frame at t = 20000 ps<br>
<font color="#3333ff">Starting time for run is 0 ps</font><br>
Calculating fourier grid dimensions for X Y Z<br>
Using a fourier grid of 72x56x75, spacing 0.111 0.114 0.117<br>
splitting topology...<br>
Walking down the molecule graph to make shake-blocks<br>
There are 14390 charge group borders and 12308 shake borders<br>
There are 12308 total borders<br>
Division over nodes in atoms:<br>
10455 10455 10455 10455<br>
writing run input file...<br>
</font><br>
###############################################################<br>
<br>
Dallas B. Warren wrote:
<blockquote
cite="mid89907EA1DCFB7548A431C13A270F9DD501D9E206@prk-exch-01.vcp.local"
type="cite">
<blockquote type="cite">
<pre wrap="">So I am generating .tpr file as follows using the command as follows.
</pre>
</blockquote>
<pre wrap=""><!---->Does the log message (Highlighted in RED)
</pre>
<blockquote type="cite">
<pre wrap="">"Velocities generated: ignoring velocities in input trajectory", means
</pre>
</blockquote>
<pre wrap=""><!---->that the simulation wont be continuation
</pre>
<blockquote type="cite">
<pre wrap="">of the earlier one?
</pre>
</blockquote>
<pre wrap=""><!---->
That warning tells you that in your .mdp file you have velocity
generation on, turn that option off. You don't want that if you want a
continuation of the run. The velocity of the atoms is taken from the
.trr file that you feed to grompp.
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
<a class="moz-txt-link-abbreviated" href="mailto:dallas.warren@vcp.monash.edu.au">dallas.warren@vcp.monash.edu.au</a>
+61 3 9903 9524
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
</pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Sridhar Acharya, M
Senior Research Fellow
Lab of Computational Biology
CDFD, Gandipet Campus
Hyderabad. AP. INDIA
<a class="moz-txt-link-freetext" href="http://www.cdfd.org.in">http://www.cdfd.org.in</a>
email: <a class="moz-txt-link-abbreviated" href="mailto:sridhar@cdfd.org.in">sridhar@cdfd.org.in</a>
Phone: Lab: 08413-235467*2044
Mobile: 9866147193
</pre>
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