[gmx-users] the position_restraints
Justin A. Lemkul
jalemkul at vt.edu
Wed Apr 15 01:13:40 CEST 2009
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: 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
>>
>> ========================================
>> _______________________________________________
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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
> 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 gmx-users-request at gromacs.org.
> 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
========================================
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