Thanks a lot! :) <br><br><div><span class="gmail_quote">On 5/10/06, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
karamyog singh wrote:<br>> Greeting gromacs users. I am trying to use gromacs to simulate metals. I<br>> am trying to simulate BCC Iron. But I get the following error message.<br>><br>> Fatal error: Invalid order for directive moleculetype, file
<br>> ""topol.top"", line 5<br><br>read chapter 5 in the manual about topology files.<br><br>><br>> I am sending you my input files. Please help me and tell me what is<br>> wrong with my files. Also can you tell me if it is possible to simulate
<br>> metallic crystals using gromacs. Mostly people have worked on Bio<br>> Molecules. However I believe that I should be able to simulate Metallic<br>> structures if I modify the source codes a bit. Also, Can you please tell
<br>> me if I can use my own potential functions?<br>Depends on what you want. CHeck manual on tabulated functions.<br><br><br>><br>> I downloaded force fields made by other people, I have modified them<br>> too to include xb_1 bond type and FE FE interaction. These modifications
<br>> have been done in ffG53a6.rtp and ffG53a6bon.itp. These files are in<br>> 53a6.tar.gz on the force field download section of the website<br>> <a href="http://www.gromacs.org">www.gromacs.org</a> <<a href="http://www.gromacs.org">
http://www.gromacs.org</a>>.<br>><br>> I request you to please help me out as soon as you can. :)<br>><br>><br>> ------------------------------------------<br>> grompp.mdp<br>><br>> NES STARTING WITH ';' ARE COMMENTS
<br>> title = Minimization of Hen Egg White Lysozyme (1AKI.pdb)<br>> ; Title of run<br>><br>> ; The following lines tell the program the standard locations where to<br>> find certain files<br>>
cpp
= /lib/cpp ; Preprocessor<br>>
include =
-I../top ; Directories to include in
the topology<br>> format<br>><br>> ; Parameters describing what to do, when to stop and what to save<br>>
integrator =
steep ; Algorithm
(steep = steepest descent<br>> minimization)<br>>
emtol =
1.0 ; Stop
minimization when the maximum<br>> force < 1.0 kJ/mol<br>>
nsteps =
200 ;
Maximum number of (minimization) steps<br>> to perform<br>>
nstenergy =
10 ;
Write energies to disk every nstenergy<br>> steps<br>>
nstxtcout =
10 ;
Write coordinates to disk every<br>> nstxtcout steps<br>>
xtc_grps =
Protein ; Which coordinate group(s)
to write to disk<br>>
energygrps =
Protein ; Which energy group(s) to
write to disk<br>><br>> ; Parameters describing how to find the neighbors of each atom and how<br>> to calculate the interactions<br>>
nstlist =
5
; Frequency to update the neighbor list<br>> and long range forces<br>>
ns_type =
simple ; Method to
determine neighbor list<br>> (simple, grid)<br>>
rlist =
1.0 ;
Cut-off for making neighbor list<br>> (short range forces)<br>> coulombtype = cut-off ; Treatment of long range electrostatic<br>> interactions<br>>
rcoulomb =
1.0 ; long
range electrostatic cut-off<br>>
rvdw =
1.0 ; long
range Van der Waals cut-off<br>> constraints
= none ;
Bond types to replace by constraints<br>>
pbc
= yes ;
Periodic Boundary Conditions (yes/no)<br>> ----------------------------------------------<br>> topol.top<br>> #include "ffG53a6.itp"<br>> ;#include "ffgmx.rtp"<br>> ;#include "ffgmx.atp
"<br>><br>> [ moleculetype ]<br>> Ions 3<br>><br>> [ atoms ]<br>> 1 Fe 1 HEME
FE
1 0 55.870<br>> 2 Fe 2 HEME
FE
1 0 55.870<br>> 3 Fe 3 HEME
FE
1 0 55.870<br>> 4 Fe 4 HEME
FE
2 0 55.870<br>> 5 Fe 5 HEME
FE
2 0 55.870<br>> 6 Fe 6 HEME
FE
2 0 55.870<br>> 7 Fe 7 HEME
FE
2 0 55.870<br>> 8 Fe 8 HEME
FE
3 0 55.870<br>> 9 Fe 9 HEME
FE
3 0 55.870<br>><br>> [ bonds ]<br>><br>> 1 2 1 0.1000 1.7800e+7<br>> --------------------------------------------------<br>> Pure Fe<br>> 9<br>> 1Fe FE 1 0.00 0.00 0.00 0.000 0.000
0.000<br>> 2Fe FE 2 2.70 0.00 0.00 0.000 0.000 0.000<br>> 3Fe FE 3 0.00 2.70 0.00 0.000 0.000 0.000<br>> 4Fe FE 4 0.00 0.00 2.70 0.000 0.000 0.000<br>> 5Fe FE 5 0.00 2.70 2.70
0.000 0.000 0.000<br>> 6Fe FE 6 2.70 0.00 2.70 0.000 0.000 0.000<br>> 7Fe FE 7 2.70 2.70 0.00 0.000 0.000 0.000<br>> 8Fe FE 8 2.70 2.70 2.70 0.000 0.000 0.000<br>> 9Fe FE 9
1.35 1.35 1.35 0.000 0.000 0.000<br>><br>><br>> conf.gro<br>><br>><br>><br>><br>> ------------------------------------------------------------------------<br>><br>> _______________________________________________
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http://www.gromacs.org/mailing_lists/users.php</a><br><br><br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>_______________________________________________
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</a><br></blockquote></div><br>