Thanks for reply. <br>I've used editconf to define the box by issuing :-<br>editconf -f popc.pdb -o popc_box.gro -c -d 1.0 -bt cubic<br>Is this the correct way of using editconf?<br>And with this i proceed with grompp with the mdp file from previous email followed by mdrun....<br>
<br>Actually the restraint is require in another system (membrane+protein), i wanted to test it out in the this smaller systme before using it in the complete systme.However, it failed.<br><br>Thanks in advance<br><br>regards,<br>
bing<br><br><br><div class="gmail_quote">On Tue, Jun 23, 2009 at 10:21 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="h5"><br>
<br>
Bing Bing wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Justin,<br>
I've tried with no restraint and the minimization stopped at the same time. I actually suspect that the restraint is not working at all. My top file is as below:-<br>
#include "ffG53a6_lipid.itp"<br>
#include "popc.itp"<br>
#ifdef POSRES<br>
#include "posres_popc.itp"<br>
#endif<br>
#ifdef FLEX_SPC<br>
#include "flexspc.itp"<br>
#else<br>
#include "spc.itp"<br>
#endif<br>
<br>
[ system ]<br>
; name<br>
Pure POPC bilayer with 128 lipids 2460 water<br>
<br>
[ molecules ]<br>
; name number<br>
POPC 128<br>
SOL 2460<br>
<br>
my posres_popc.itp is as below:-<br>
[ position_restraints ]<br>
; atom type fx fy fz<br>
1 1 1000 1000 1000<br>
.....<br>
51 1 1000 1000 1000<br>
52 1 1000 1000 1000<br>
<br>
my mdp file as below :-<br>
define = -DPOSRES<br>
integrator = steep<br>
emtol = 1000<br>
emstep = 0.01<br>
nsteps = 100<br>
rlist = 1.2<br>
coulombtype = PME<br>
rcoulomb = 1.2<br>
rvdw = 1.2<br>
constraints = none<br>
<br>
May i know that is the top, posres and also the mdp file correctly done?<br>
</blockquote>
<br></div></div>
Well, they are syntactically correct, it seems. I see no purpose in restraining lipids during a minimization, however.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
And by looking at the log file in the previous mail, is it confirm that it manage to read the restraint file?<br>
</blockquote>
<br></div>
Can't tell. Your system is crashing instantly for some reason.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
The starting structure is taken from Peter Tielemen website and what i did is editconf to make box and i didn't solvate because the starting structure come together with water. I'm not sure this is the correct way of doing it. Please advice.<br>
</blockquote>
<br></div>
Please define "editconf to make box" - have you somehow manipulated the structure? That could be a source of error. The structure that Tieleman provides minimized for me with no problem when I used it recently.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
Thanks in advance.<br>
Bing<div><div></div><div class="h5"><br>
<br>
<br>
On Tue, Jun 23, 2009 at 7:16 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Bing Bing wrote:<br>
<br>
Hi! I'm a postgraduate student from Malaysia and currently<br>
facing energy minimization problem for my membrane system.<br>
I'm trying to perform energy minimization for an empty POPC<br>
membrane with position restraint on the lipid. Minimization stop<br>
due to inf Fmax. And I noticed that in the log file as below:-<br>
Initiating Steepest Descents<br>
Max number of connections per atom is 25<br>
Total number of connections is 84976<br>
Max number of graph edges per atom is 4<br>
Total number of graph edges is 22896<br>
Going to use C-settle (2460 waters)<br>
wo = 0.333333, wh =0.333333, wohh = 3, rc = 0.08165, ra = 0.0384897<br>
rb = 0.0192448, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1<br>
Started Steepest Descents on node 0 Tue Jun 23 17:03:43 2009<br>
Steepest Descents:<br>
Tolerance (Fmax) = 1.00000e+03<br>
Number of steps = 100<br>
Grid: 11 x 11 x 11 cells<br>
Step Time Lambda<br>
0 0.00000 0.00000<br>
Energies (kJ/mol)<br>
Bond Angle Proper Dih. Ryckaert-Bell.<br>
Improper Dih.<br>
1.64082e+05 1.71875e+04 4.06560e+03 6.45104e+03 8.36392e+03<br>
LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip.<br>
2.12067e-314 2.12067e-314 -1.58963e+04 -1.05392e+05 -1.15292e+05<br>
Position Rest. Potential Pressure (bar)<br>
0.00000e+00 -3.64297e+04 nan<br>
<br>
<br>
>From the looks of some of these energies (i.e., LJ-14,<br>
Coulomb-14), it looks like something is severely wrong with your<br>
starting structure, and applying position restraints probably isn't<br>
helping.<br>
<br>
Try the minimization without restraints and see if it works.<br>
<br>
Also, have you set the appropriate "define" line in the .mdp file,<br>
corresponding to what is prescribed in the .top?<br>
<br>
-Justin<br>
<br>
-------------------------------------------------------<br>
Program mdrun_d, VERSION 4.0.5<br>
Source code file: nsgrid.c, line: 357<br>
Range checking error:<br>
Explanation: During neighborsearching, we assign each particle<br>
to a grid<br>
based on its coordinates. If your system contains collisions or<br>
parameter<br>
errors that give particles very high velocities you might end up<br>
with some<br>
coordinates being +-Infinity or NaN (not-a-number). Obviously,<br>
we cannot<br>
put these on a grid, so this is usually where we detect those<br>
errors.<br>
Make sure your system is properly energy-minimized and that the<br>
potential<br>
energy seems reasonable before trying again.<br>
Variable ci has value -2147483648. It should have been within [<br>
0 .. 1331 ]<br>
the position restraint energy is 0 as highlighted. Here's the<br>
position restraint file :-<br>
[ position_restraints ]<br>
; atom type fx fy fz<br>
1 1 1000 1000 5000<br>
5 1 1000 1000 1000<br>
6 1 1000 1000 1000<br>
7 1 1000 1000 1000<br>
8 1 1000 1000 1000<br>
9 1 1000 1000 1000<br>
10 1 1000 1000 1000<br>
......<br>
<br>
whereby the restraint energy is 1000kcal/mol in x, y and z<br>
plane. In the log file the position restraint energy is stated<br>
as 0.0000e+00 (as highlighted above).<br>
I think that the position restraint is not working fine here. Is<br>
there anyways to solve this? did I miss out something here?<br>
I would be grateful if anyone can advice me on this.<br>
<br>
------------------------------------------------------------------------<br>
<br>
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<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><br>
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