[gmx-users] the position_restraints
He, Yang
yang.he at mavs.uta.edu
Wed Apr 15 00:50:27 CEST 2009
Hi Justin,
I will list my mdp file below:
integrator = sd
dt = 0.001
nsteps = 200000
comm_mode = Linear ; Linear, None, Angular
nstcomm = 0
comm-grps = System
nstfout = 0
nstxout = 1000
nstvout = 1000
nstlog = 1000nstenergy = 100
nstxtcout = 100
xtc_grps = System
energygrps = DNA
energygrp_excl =
nstlist = 0
ns_type = simple
pbc = no ; xyz, no (vacuum), full (infinite)
rlist = 0
coulombtype = Cut-off
rcoulomb = 0
vdwtype = Cut-off
rvdw = 0
tcoupl = no ; for sd, tcoupl is ignored
tc-grps = System
tau_t = 0.0347
ref_t = 270
pcoupl = no
gen_vel = yes
gen_temp = 300
gen_seed = 173529
constraints = none ; none, all-bonds
freezegrps =
freezedim =
Thank you for your further suggestion.
Yang
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Tuesday, April 14, 2009 3:29 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] the position_restraints
He, Yang wrote:
> HI Justin,
>
> I just use the mdrun command and then get such error. Before that, I did not get other messages just go on well expect when I use the mdrun.
>
> Also, when I did not use the position_restraints , it will run smoothly. As long as I add this even though the position_restraints includes only one atom, it will show the error.
>
This is difficult to diagnose exactly. To me, removal of position restraints
suggests that you are fixing in place some bad contact that is causing your
system to crash. Have a look at the trajectory to see what is going on. Did EM
work properly? If you are still having trouble, post a more complete
description of your system, relevant .mdp file(s), and anything else necessary
to try to get a resolution.
-Justin
> Yang
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Tuesday, April 14, 2009 3:06 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] the position_restraints
>
> He, Yang wrote:
>> HI all users,
>>
>> I want to define the position_restraints in the itp file but when I run it, it always show that
>>
>> Segmentation fault (core dumped)
>>
>
> You'll have to do better than "run it" - what do you mean, grompp? mdrun?
>
> As written, your position restraints look OK, so I don't think the problem is
> related to that section, necessarily. How have you deduced that this is where
> the problem lies?
>
> Are you getting any other messages from (grompp? mdrun?) before the seg fault?
>
> -Justin
>
>> and I will list the part below:
>>
>> [position_restraints]
>> ;ai funct fc
>> 1 1 10000 10000 10000
>> 2 1 10000 10000 10000
>> 3 1 10000 10000 10000
>> 4 1 10000 10000 10000
>> 5 1 10000 10000 10000
>> 6 1 10000 10000 10000
>> 7 1 10000 10000 10000
>> 8 1 10000 10000 10000
>> 9 1 10000 10000 10000
>> 10 1 10000 10000 10000
>> 11 1 10000 10000 10000
>> 12 1 10000 10000 10000
>> 13 1 10000 10000 10000
>> 14 1 10000 10000 10000
>> 15 1 10000 10000 10000
>> 16 1 10000 10000 10000
>> 17 1 10000 10000 10000
>> 18 1 10000 10000 10000
>> 19 1 10000 10000 10000
>> 20 1 10000 10000 10000
>> 41 1 10000 10000 10000
>> 42 1 10000 10000 10000
>> 43 1 10000 10000 10000
>> 44 1 10000 10000 10000
>> 45 1 10000 10000 10000
>> 46 1 10000 10000 10000
>> 47 1 10000 10000 10000
>> 48 1 10000 10000 10000
>> 49 1 10000 10000 10000
>> 50 1 10000 10000 10000
>> 51 1 10000 10000 10000
>> 52 1 10000 10000 10000
>> 53 1 10000 10000 10000
>> 54 1 10000 10000 10000
>> 55 1 10000 10000 10000
>> 56 1 10000 10000 10000
>> 57 1 10000 10000 10000
>> 58 1 10000 10000 10000
>> 59 1 10000 10000 10000
>> 60 1 10000 10000 10000
>>
>> Can anyone of you tell me what is the problem for that? Thank you very much in advance.
>>
>> Yang
>> _______________________________________________
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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