Thanks for your comments.<br>One more question.<br>Does Gromacs saves velocities in pdb files, when we use gen_vel=yes option in mdp and save the output(-c) of mdrun as pdb file instead of gro file.<br><br><div class="gmail_quote">
On Fri, Apr 6, 2012 at 19:48, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"><div class="im">
On 7/04/2012 12:15 AM, bipin singh wrote:
<blockquote type="cite"><a name="1368805b5b524292_vel">When we mention<br>
gen_vel=no ;And provide pdb as input with no velocities<br>
</a><a name="1368805b5b524292_vel"><br>
As mentioned in the manual:</a><a name="1368805b5b524292_vel"><br>
"The velocities are set to zero
when there are no velocities in the input structure file"<br>
<br>
</a>Please elaborate what does this sentence mean.<br>
</blockquote>
<br></div>
Each atom must have a velocity in a *dynamical* simulation. If there
is no instruction for what values to use (i.e. not generated or
supplied), zero is used. Integration proceeds from there, and this
may or may not be stable, and certainly will not have the desired
temperature (yet)...<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div><div class="h5"><br>
<br>
<blockquote type="cite"><br>
<div class="gmail_quote">On Fri, Apr 6, 2012 at 19:10, Justin A.
Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><br>
<br>
bipin singh wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Also, if we give continuation=yes in mdp file and use
input as pdb file as input instead of gro file, grompp
never complains....I don't no how it reads velocities from
pdb file (as no velocities are present in pdb files).
Ideally it should complain that no velocities found in
input file....<br>
<br>
</blockquote>
<br>
</div>
Again, the "continuation" keyword has nothing to do with
velocities. If you have "gen_vel = no" and you provide a .pdb
file with no velocities, then you do not preserve velocity
information. Whatever the initial forces are govern the
resulting motions. In any case, you do not preserve the
previous simulation conditions.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div>
On Fri, Apr 6, 2012 at 12:42, Peter C. Lai <<a href="mailto:pcl@uab.edu" target="_blank">pcl@uab.edu</a> <mailto:<a href="mailto:pcl@uab.edu" target="_blank">pcl@uab.edu</a>>> wrote:<br>
<br>
On 2012-04-06 11:05:51AM +0400, James Starlight
wrote:<br>
> Dear Gromacs users!<br>
><br>
><br>
> I have small question about order of the runs
and input data.<br>
><br>
> Ussually I do 2 equilibration phases and
subsequent productive<br>
phase in the<br>
> conditions wich are equal to the last
equilibration phase ( e.g<br>
often this<br>
> is npt ).<br>
><br>
> In the second equil.mdp and md.mdp there is
option<br>
><br>
> continuation = yes<br>
><br>
> which means that there have been previous
phases of the<br>
simulation from<br>
> wich coordinates and velocities should be
taken.<br>
><br>
> As I understood the coordinates is taken from
.gro file but from<br>
what file<br>
> the velocities must be providen ? Does it .cpt
checkpoint file from<br>
> previous run? In some cases I've forgotten to
define -t npt.cpt<br>
for my MD<br>
> run providing only coordinates in GRO file,
topology and md.mdp<br>
but I have<br>
> not seen any errors in such simulation due to
absence of that<br>
.cpt and<br>
> GROMPP never remind me of the absense of this
file. What exactly<br>
is in that<br>
> .cpt file and from wich source the velocities
from equilibration<br>
phase are<br>
> taken ?<br>
<br>
continuation = yes is telling LINCS that it is a
continuation and<br>
it should not attempt to refit the constrained bonds
on the first pass.<br>
<br>
The coords, velocities, state, and box information
are taken either<br>
from the<br>
cpt file or you can specify the previous .trr and it
will take the<br>
last frame<br>
from that and use it. If you used the output gro file
without -t, then<br>
it will take coordinates and velocities from the .gro
but the<br>
problem there<br>
is the limited precision (3 decimal points for each).<br>
<br>
--<br>
==================================================================<br>
Peter C. Lai | University of
Alabama-Birmingham<br>
Programmer/Analyst | KAUL 752A<br>
Genetics, Div. of Research | 705 South 20th
Street<br>
</div>
</div>
<a href="mailto:pcl@uab.edu" target="_blank">pcl@uab.edu</a> <mailto:<a href="mailto:pcl@uab.edu" target="_blank">pcl@uab.edu</a>> |
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<br>
<span><font color="#888888">
</font></span></blockquote>
<span><font color="#888888">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></font></span>
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<span style="color:rgb(51,51,255)">-----------------------</span><br style="color:rgb(51,51,255)">
<i><span style="color:rgb(51,51,255)">Regards,</span></i><br style="color:rgb(51,51,255)">
<span style="color:rgb(51,51,255);font-family:garamond,serif">Bipin
Singh</span><br>
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<i><span style="color:rgb(51,51,255)">Regards,</span></i><br style="color:rgb(51,51,255)"><span style="color:rgb(51,51,255);font-family:garamond,serif">Bipin Singh</span><br><br>