<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
</style>
</head>
<body class='hmmessage'>
Are you sure your initial distance is -3.5 along (0,0,-1),<br>this means the distance is actually +3.5 in z.<br><br>Another issue could be that 3.5 is more than half the box size.<br>I think we should add a check for too long distances,<br>so users get a clear error message and they do not need to contact<br>the mailing list.<br><br>Berk<br><br>> Date: Wed, 9 Sep 2009 13:18:04 -0400<br>> From: hideyanakamura@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Errors in constraint pulling<br>> <br>> Dear GROMACS users,<br>> <br>> I am trying to calculate the potential of mean force (PMF) of a<br>> molecule (A) across phospholipid bilayer (LIP) using constraint<br>> method.<br>> I am using GROMACS ver 4.0.4.<br>> RUN parameters are as follows<br>> -------------------------------------------------------------------------------<br>> integrator = md<br>> tinit = 0<br>> dt = 0.002 ;[ps]<br>> nstlist = 10 ;[step]<br>> ns_type = grid<br>> rlist = 1.0<br>> pbc = xyz<br>> <br>> coulombtype = pme<br>> rcoulomb = 1.0 [nm]<br>> epsilon-r = 1 ;(1)<br>> vdw-type = switch<br>> rvdw-switch = 0.9 ;[nm]<br>> rvdw = 1.0 ;[nm]<br>> DispCorr = EnerPres<br>> <br>> fourierspacing = 0.12 ;[nm] (0.12)<br>> fourier_nx = 0 ;(0)<br>> fourier_ny = 0 ;(0)<br>> fourier_nz = 0 ;(0)<br>> pme_order = 4 ;(4)<br>> ewald_rtol = 1e-05 ;(1e-5)<br>> epsilon_surface = 0 ;(0)<br>> optimize_fft = no<br>> <br>> tcoupl = berendsen<br>> tc_grps = LIP SOL A<br>> tau_t = 0.1 0.1 0.1 ;[ps]<br>> ref_t = 300 300 300 ;[K]<br>> Pcoupl = berendsen<br>> Pcoupltype = semiisotropic ;useful for membrane <br>> tau_p = 1.0 1.0 ;[ps]<br>> compressibility = 4.5e-05 4.5e-05 ;[bar^-1]<br>> ref_p = 1.0 1.0 ;[bar]<br>> <br>> gen_vel = no ;yes or no<br>> gen_temp = 300 ;[K]<br>> gen_seed = 113 ;(173529)<br>> <br>> constraints = all-bonds ;all-bonds/none<br>> constraint-algorithm = LINCS<br>> unconstrained-start = no<br>> lincs-order = 4 ;(4)<br>> lincs-warnangle = 30 ;(30)<br>> <br>> ; COM PULLING<br>> pull = constraint<br>> pull_geometry = direction<br>> pull_dim = N N Y<br>> pullstart = no<br>> pull_nstxout = 10<br>> pull_nstfout = 10<br>> pull_ngroups = 1<br>> pull_group0 = LIP<br>> pull_group1 = A<br>> pull_vec1 = 0.0 0.0 -1.0<br>> pull_init1 = -3.50<br>> pull_rate1 = 0<br>> pull_k1 = 500<br>> -------------------------------------------------------------------------------<br>> When I simulated under above parameters, following warnings and errors<br>> were generated.<br>> <br>> -Warning: pressure scaling more than 1%<br>> -LINCS warning:<br>> <br>> These errors were always generated when a molecule (pull_gropu1) was<br>> existing in water phase.<br>> After simulation, serious disruption of a molecule (pull_gropu1) was observed.<br>> <br>> However, when a molecule (pull_gropu1) was existing inside lipid<br>> membrane, no error was observed and calculation was successfully<br>> conducted in constrained simulation.<br>> <br>> I have done long time (5 nsec) simulations before constrained<br>> simulation using umbrella method, thus I believe the initial condition<br>> is fully equilibrated.<br>> <br>> Could some one please give me an advice to calculate PMF?<br>> <br>> Sincerely<br>> <br>> <br>> ___________________________________________________________________<br>> Hideya Nakamura, Ph.D.<br>> <br>> Post Doctoral Associate<br>> University of Florida, Particle Engineering Research Center (PERC)<br>> mail to: hideyanakamura@gmail.com<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.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>