[gmx-users] Re: gmx-users Digest, Vol 86, Issue 183

[Thereza Soares]

Hi Justin,

I have used the same files to re-run using gromacs-4.5.4 and the only difference is that I get a "segmentation fault" instead of "bus error" message.
Thanks for your help, I will then fill out the issue report as you suggested.

Best,

Thereza

Professor Thereza A. Soares
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Av. Jornalista Anibal Fernandes, s/nº 
Cidade Universitária 50740-560
Recife, PE, Brazil
tel: +558121268440
fax: +558121268442
thereza.soares at ufpe.br
website at dqf
http://dqfnet.ufpe.br/biomat/


On Jun 27, 2011, at 12:06 PM, gmx-users-request at gromacs.org wrote:

> 
> Date: Mon, 27 Jun 2011 10:28:46 -0300
> From: Thereza Soares <thereza.soares at ufpe.br>
> Subject: [gmx-users] Comparing MD ensembles with exp. NOE restraints
> 	--> bus	error
> To: gmx-users at gromacs.org
> Message-ID: <032EC9E3-5B6E-466C-A785-3ADFC44F4F7B at ufpe.br>
> Content-Type: text/plain; charset=windows-1252
> 
> Hi There,
> 
> I would like to compare my ensemble of (unrestrained) MD structures against experimental NOE distances. For that, I have added the distance_restraints block to my *.top file such as:
> 
> [distance_restraints]
> ;ai    aj type index type‚ low   up1 up2 fac
> 33    31    1    0    1  0.0  3.000 1.2 0.4 
> 35    31    1    1    1  0.0  2.500 0.7 0.3  
> 
> I have also added the disre options below to the *.mdp file used to generate a new tpr for the NOE analysis 
> 
> disre             = Simple
> disre-weighting   = Equal
> disre-mixed       = no
> disre-fc          = 1000
> disre-tau         = 0
> nstdisreout       = 1
> 
> When I run g_disre -s proton.tpr -f trj.pdb, it reads the tpr file and gives a bus error ... I am copying the entire mdp file in case someone can point me out what is wrong with it.
> 
> 
> I would appreciate any suggestions on what maybe wrong here,
> 
> Cheers,
> 
> Thereza
> 
> integrator               = md
> dt                       = 0.002
> nsteps                   = 25000000
> nstxout                  = 500
> nstvout                  = 500
> nstlog                   = 500 
> nstenergy                = 500
> nstxtcout                = 500
> comm-mode                = Linear
> nstcomm                  = 5
> comm-grps                = SYSTEM  
> xtc_grps                 = SYSTEM
> energygrps               = SYSTEM
> nstlist                  = 5
> rlist                    = 1.4
> coulombtype              = generalized-reaction-field
> epsilon_rf               = 66.0
> ns_type                  = grid
> rcoulomb                 = 1.4
> rvdw                     = 1.4
> pbc                      = xyz
> tcoupl                   = berendsen
> tc-grps                  = SYSTEM
> tau_t                    = 0.2 
> ref_t                    = 300 
> Pcoupl                   = berendsen
> Pcoupltype               = semi-isotropic
> tau_p                    = 0.4 0.4 
> compressibility          = 4.5e-5 4.5e-5 
> ref_p                    = 1.0 1.0
> gen_vel                  = yes 
> gen_temp                 = 10
> gen_seed                 = 178296
> constraints              = h-bonds
> disre             = simple
> disre-weighting   = equal
> disre-mixed       = no
> disre-fc          = 1000
> disre-tau         = 0
> nstdisreout       = 1
> 
> 
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Mon, 27 Jun 2011 09:49:29 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Comparing MD ensembles with exp. NOE
> 	restraints -->	bus	error
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E088A69.7080902 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
> 
> 
> 
> Thereza Soares wrote:
>> Hi There,
>> 
>> I would like to compare my ensemble of (unrestrained) MD structures against
>> experimental NOE distances. For that, I have added the distance_restraints
>> block to my *.top file such as:
>> 
>> [distance_restraints] 
>> ;ai    aj type index type‚ low   up1 up2 fac
>> 33    31    1    0    1  0.0  3.000 1.2 0.4
>> 35    31    1    1    1  0.0  2.500 0.7 0.3
>> 
>> 
>> I have also added the disre options below to the *.mdp file used to generate
>> a new tpr for the NOE analysis
>> 
>> disre             = Simple 
>> disre-weighting   = Equal
>> disre-mixed       = no
>> disre-fc          = 1000 
>> disre-tau         = 0
>> nstdisreout       = 1
>> 
>> When I run g_disre -s proton.tpr -f trj.pdb, it reads the tpr file and gives
>> a bus error ... I am copying the entire mdp file in case someone can point me
>> out what is wrong with it.
>> 
> 
> There is nothing wrong with the .mdp file.  There is likely a bug in the g_disre 
> code somewhere, as is usually the case with immediate bus errors or segmentation 
> faults.
> 
>> 
>> I would appreciate any suggestions on what maybe wrong here,
>> 
> 
> You haven't mentioned which version of Gromacs you're using, but if it is not 
> 4.5.4 (the latest), please try again with this version.  If you are using 4.5.4 
> or the error persists, please file an issue report on redmine.gromacs.org and 
> include your .tpr and .pdb files necessary to reproduce the problem.
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
>