<font color="#000099"><font face="verdana,sans-serif">Thanks, I will try to figure it out.<br></font></font><br><div class="gmail_quote">On Tue, Nov 15, 2011 at 9:50 PM, 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 bgcolor="#FFFFFF" text="#000000"><div class="im">
On 16/11/2011 2:45 PM, Liu, Liang wrote:
<blockquote type="cite"><font color="#000099"><font face="verdana,sans-serif">Thanks
for help.</font></font>
<div><font color="#000099"><font face="verdana,sans-serif">If I
have more atoms and they can interact each other or itself,
like PP, PC, PN, CP, CN, CC .... How's the energygrp_table
looking like?</font></font></div>
<div><font color="#000099" face="verdana,
sans-serif">I know there should be a option in the grompp, but
how to do that?</font></div>
</blockquote>
<br></div>
See manual sections 7.3.12 and 6.7.2.<div class="im"><br>
<br>
<blockquote type="cite">
<div><font color="#000099" face="verdana,
sans-serif"> And how to generate the index file? I am sorry
for so many questions, I am really not familiar with it.</font></div>
</blockquote>
<br>
</div><a href="http://www.gromacs.org/Documentation/File_Formats/Index_File" target="_blank">http://www.gromacs.org/Documentation/File_Formats/Index_File</a><span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div><div class="h5"><br>
<br>
<blockquote type="cite">
<div><br>
<div class="gmail_quote">On Tue, Nov 15, 2011 at 9:28 PM,
Sikandar Mashayak <span dir="ltr"><<a href="mailto:symashayak@gmail.com" target="_blank">symashayak@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
>From your system information, I understand that you need
to specify tabulated potentials between atoms P and P, and
between atoms C and P, and so on. <br>
<br>
To achieve this, you need to create energy groups with atom
types P and C, and specify energygrp_table options in the
grompp such as following<br>
<br>
....<br>
<br>
energygrps = P C ; (and rest of the groups in your system,
you will need to specify index file containing energy groups
) <br>
energygrp_table = P P P C<br>
<br>
....<br>
<br>
so now mdrun looks for table_P_P.xvg and table_P_C.xvg in
the run directory, and uses it for P-P and P-C interactions,
whereas for all other interactions default table.xvg file is
used.<br>
<br>
<br>
I hope this helps.<br>
<br>
Regards<br>
Sikandar<br>
<br>
<br>
<div class="gmail_quote">
<div>
<div>On Tue, Nov 15, 2011 at 2:49 PM, Liu,
Liang <span dir="ltr"><<a href="mailto:liu4gre@gmail.com" target="_blank">liu4gre@gmail.com</a>></span>
wrote:<br>
</div>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div><font color="#000099"><font face="verdana,sans-serif">I am trying to use a
serial of tabulated potentials, which are the
functions of the distance between atoms and the
names are table.xvg, table_P_P.xvg,
table_C_P.xvg, etc., to do the energy
minimization of some RNA structures.</font></font>
<div>
<font color="#000099"><font face="verdana,sans-serif">The procedure I
apply is as following:</font></font></div>
<div><font color="#000099"><font face="verdana,sans-serif"><br>
</font></font></div>
<div><font color="#000099"><font face="verdana,sans-serif">
<div>
pdb2gmx -f rna.pdb -o conf.pdb -ff amber03
-water spce</div>
<div>editconf -bt octahedron -f conf.pdb -o
box.pdb -d 1.0</div>
<div>genbox -cp box.pdb -cs spc216 -o
water.pdb -p topol.top</div>
<div>grompp -f em.mdp -c water.pdb -p
topol.top -o em.tpr -maxwarn 2</div>
<div>mdrun -v -s em.tpr -c em.pdb -table
table.xvg</div>
<div><br>
</div>
<div>And the em.mdp file is:</div>
<div>
<div>cpp = /usr/bin/cpp
; Preprocessor</div>
<div>include = -I../top
; Directories to include in the
topology format</div>
<div>define = -DFLEX_SPC</div>
<div>integrator = steep
; Algorithm options</div>
<div>dt = 0.002 ; ps !
; run control, the time step</div>
<div>nsteps = 1000
; run steps, simulation length =
dt*nsteps</div>
<div>nstenergy = 10
; Write energies to disk every
nstenergy steps</div>
<div>nstxtcout = 10
; Write coordinates to disk every
nstxtcout steps</div>
<div>xtc_grps = RNA
; Which coordinate group(s) to
write to disk</div>
<div>energygrps = RNA
; Whici energy group(s) to write
to disk</div>
<div>nstlist = 10
; Frequency to update the neighbor
list and long range forces</div>
<div>
ns_type = grid
; Method to determine neighbor list
and long range forces (simple, grid)</div>
<div>rlist = 1.0
; Cut-off for making neighbor list
(short range forces)</div>
<div>vdw-type = user</div>
<div>coulombtype = user
; Treatment of long range
electrostatic interactions</div>
<div>rcoulomb = 1.0
; long range electrostatic cut-off</div>
<div>rvdw = 1.0
; long range Van der Walls cut-off</div>
<div>constraints = none</div>
<div>pbc = xyz</div>
<div>emtol = 5000.0</div>
<div>emstep = 0.01</div>
</div>
</font></font>
<div><br>
</div>
<div>All the procedure and file are right? Thanks.</div>
<span><font color="#888888">
<div><br>
</div>
-- <br>
Best,<br>
Liang Liu<br>
</font></span></div>
<br>
</div>
</div>
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<br>
<br clear="all">
<div><br>
</div>
-- <br>
Best,<br>
Liang Liu<br>
</div>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div></div>
<br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Best,<br>Liang Liu<br>