<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
FONT-SIZE: 10pt;
FONT-FAMILY:Tahoma
}
</style>
</head>
<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>There can be many reasons for such problems.<br>I assume you use solvent.<br><br>One option is that you could have made your whole protein<br>a single charge group. grompp in Gromacs 3.3.3 checks for this,<br>but older versions do not.<br></div><br>Berk.<br><br><br><hr id="stopSpelling">> From: affinito@gmail.com<br>> To: gmx-users@gromacs.org<br>> Date: Thu, 8 May 2008 14:54:27 +0200<br>> Subject: [gmx-users] crash nsgrid.c<br>> <br>> <br>> Dear all,<br>> During my simulations of a GFP protein (force field made with amber, <br>> then converted to gromacs), I usually get this error:<br>> <br>> Fatal error: ci = 8108 should be in 0 .. 7937 [FILE nsgrid.c, LINE 218]<br>> <br>> What this that means?<br>> <br>> If I restart the simulation from the frame just before the crash, the <br>> run is ok for a (random) time and then it crashes again.<br>> I checked this on different kind of machines and I get always the same <br>> behavior.<br>> <br>> To make things clearier, I include the input.mdp file:<br>> <br>> title =<br>> cpp = /lib/cpp<br>> include =<br>> define =<br>> integrator = md<br>> dt = 0.002<br>> nsteps = 500000<br>> nstxout = 10000<br>> nstvout = 0<br>> nstlog = 500<br>> nstenergy = 500<br>> nstxtcout = 500<br>> energygrps = System<br>> pbc = xyz<br>> nstlist = 15<br>> epsilon_r = 1.<br>> ns_type = grid<br>> coulombtype = pme<br>> vdwtype = Cut-off<br>> rlist = 0.8<br>> rcoulomb = 0.8<br>> rvdw = 0.8<br>> tcoupl = Nose-Hoover<br>> tc-grps = System<br>> tau_t = 2.0<br>> ref_t = 300.00<br>> pcoupl = Parrinello-Rahman<br>> pcoupltype = isotropic<br>> tau_p = 4.0<br>> compressibility = 4.5e-5<br>> ref_p = 1.0<br>> gen_vel = no<br>> gen_seed = 173529<br>> constraints = All-bonds<br>> constraint_algorithm = lincs<br>> shake_tol = 0.0001<br>> <br>> Any suggestion is welcome.<br>> <br>> Thanks<br>> <br>> F.A.<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
</html>