[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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