<br><br> Hello Gromacs users:<br><br><br>I am running a dimeric protein simulation on Gromacs 3.3 using the force filed G43a1. <br><br><br>
For initially minimizing the hydrogen i did some small minimization and equilibration in the vacuum by maintaining the restraints <br>
then i added ions and water but in the very first minimization i m getting the following error <br>
<br>
<br>
1-4 interaction between 1 and 9 at distance 8.454 which is larger than the 1-4 table size 1.000 nm<br>
These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>
<br>
<br>
In the log file i am getting :<br>
<br>
4 inconsistent shifts check your topology <br>
<br>
following is my input file :<br>
<br>
title = 1min in water<br>
define = -DPOSRES<br>
integrator = steep<br>
dt = 0.001<br>
constraints = none<br>
nsteps = 500<br>
nstlist = 10<br>
rcoulomb = 1<br>
rlist = 1<br>
rvdw = 1.4<br>
ns_type = grid<br>
coulombtype = PME<br>
pbc = xyz<br>
gen_vel = no<br>
fourierspacing = 0.12<br>
pme_order = 6<br>
ewald_rtol = 1e-5<br>
optimize_fft = yes<br>
comm_mode = angular<br>
emtol = 100.0<br>
emstep = 0.01<br>
<br>
<br>
after adding the ions i have modified the topology file, <br>
please tell me what is the exact reason for this error or what are
the other things i should check in relation to the error <br>
<br>
With regards<br>
Thanks <br>
<br><div><span class="gmail_quote">On 7/2/07, <b class="gmail_sendername">Tsjerk Wassenaar</b> <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</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;">
Hi Fufeng Liu,<br><br>I guess you ran pdb2gmx on the two peptides, where both peptides had<br>the same chain identifiers. In that case, pdb2gmx will assume that<br>it's one molecule and connect them. Use chain identifiers to indicate
<br>the different peptides, or build topologies first on separate files<br>and combine the peptides later.<br><br>Cheers,<br><br>Tsjerk<br><br>On 7/1/07, Mark Abraham <<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au
</a>> wrote:<br>> Please keep requests for help on the list. That way they're archived for<br>> others to use, and other people can raise points of interest.<br>><br>> The last sentence here<br>> <a href="http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off">
http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off</a><br>> is my suggestion for you :-) Probably, you have only one [molecule]<br>> statement for your two molecules, and by chance you included it first so
<br>> that there was no error message from grompp. If you don't understand why<br>> this is a problem, find the relevant section of Chapter 5 of the manual -<br>> or read the whole lot of that chapter! :-)<br>
><br>> Mark<br>><br>> ---------------------------- Original Message ----------------------------<br>> Subject: How simulate two peptides in a box?<br>> From: <a href="mailto:fufengliu@tju.edu.cn">fufengliu@tju.edu.cn
</a><br>> Date: Sun, July 1, 2007 11:09 pm<br>> To: <a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a><br>> --------------------------------------------------------------------------<br>
><br>> Dear Mark:<br>> I'm a graduate student at Tianjin University. I want to simulate two<br>> peptides<br>> in a box using GROMACS software? I followed your suggestion<br>><br>> {set up your topologies (suggest one molecule in each of two .itp files)
<br>> #include them in the .top file, pick a starting configuration for both of<br>> them in the same structure file, solvate, minimize.}<br>><br>> But when I minimized the system, I got the information ¡±1-4 interaction
<br>> between 83 and 85 at distance 1.862 which is larger than the 1-4 table<br>> size 1.000 nm¡±. I checked the topology and found that atom 83 belong to<br>> one peptide and the atom 85 the other peptide. That¡¯s to say the two
<br>> peptides were considered as a peptide. Can you tell me how to do? I'd be<br>> very happy and grateful if you could tell me how to do it.<br>> Looking forward to your reply.<br>> Best regards.<br>
> Fufeng Liu<br>><br>><br>><br>><br>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search
</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read
<a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>><br><br><br>--<br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>Padualaan 8<br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931<br>F: +31-30-2537623<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search
</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read
<a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br>