He, Yang wrote:
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.
So you're doing a simulation of DNA in vacuum, I take it. Note that your
gen_temp and ref_t do not match; I don't know if this will cause problems or not.
Again, I ask - did EM complete properly? What is going on in the trajectory in
both the restrained and unrestrained simulations? It still seems to me that if
restraints induce a crash, some interaction is unrealistic and cannot be
resolved due to the strong restraints you've imposed. This part of the
diagnosis is yours to do; no one on this list can inspect your trajectories for
you. If it helps, set nstxout = 1 for diagnostic purposes.
-Justin
Yang
________________________________________
From: [email protected] [[email protected]] On Behalf
Of Justin A. Lemkul [[email protected]]
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: [email protected] [[email protected]] On Behalf
Of Justin A. Lemkul [[email protected]]
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
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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 [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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 [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
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 [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
