[gmx-users] bonds rotating more than 30 and segmentation fault.

[XAvier Periole]

you may want to have a look at the cutoff used by the force field you  
defined your
molecule in! 0.5 is definitely too small.

did you minimized?

if your starting configuration does not correspond to the topology,  
the use of position
restrains (-DPOSRES) if you actually define them will be a problem ...

> I am trying to simulate a non protein molecule and have included the  
> necessary parameters in the ff*.rtp file. I first encountered an  
> error in the grompp step, so i modified my .mdp files such that the  
> rlist, rvdw and rcoulomb values are set to 0.5. Now, while carrying  
> out the mdrun for the position restraint step, I am getting a  
> segmentation fault and a LINCS warning for the dihedrals that exceed  
> 30. I do not know how to proceed and I'm using version 3.3.3 so the  
> bug in the earlier version should have been fixed. I have also tried  
> other suggestions in the forum with no effect. Here is my pr.mdp file
>
>
> title               =  cpeptide position restraining
> warnings            =  10
> cpp                 =  /lib/cpp
> define              =  -DPOSRES
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  10000    ; total 20.0 ps.
> nstcomm             =  1
> nstxout             =  10
> nstvout             =  1000
> nstfout             =  0
> nstlog              =  10
> nstenergy           =  10
> nstlist             =  10
> ns_type             =  grid
> fourierspacing      =  0.12
> pme_order           =  4
> ewald_rtol          =  1e-5
> rlist               =  0.5
> coulombtype          =  PME
> rcoulomb            =  0.5
> rvdw                =  0.5
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tau_t               =  0.1        0.1
> tc-grps            =  Protein    other
> ref_t               =  300        300
> ; Pressure coupling is not on
> Pcoupl              =  no
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
>
>
> and this is the error I am encountering.
>
> Back Off! I just backed up md.log to ./#md.log.2#
> Reading file NOR_pr.tpr, VERSION 3.3.3 (single precision)
>
> Back Off! I just backed up ener.edr to ./#ener.edr.2#
> starting mdrun 'Protein in water'
> 10000 steps,     20.0 ps.
>
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 361281.968750 (between atoms 2 and 7) rms 231973.328125
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>       1      2   89.7    0.1530 43840.2148      0.1530
>       1      5   89.8    0.1530 44279.3516      0.1530
>       2      3   89.3    0.1530 51527.6133      0.1530
>       2      7   89.1    0.1530 55276.2969      0.1530
>       3      4   89.5    0.1530 22948.2949      0.1530
>       3      6   88.5    0.1530 20192.1895      0.1530
>       4      5   88.8    0.1530 8407.1387      0.1530
>       4      7   89.3    0.1530 26344.8340      0.1530
>       5      6   91.3    0.1530 33359.8477      0.1530
>       6      7   88.6    0.1530 13846.0684      0.1530
> Segmentation fault
>
>
> I have been trying to solve this problem for quite some time now. It  
> would be very helpful if you can suggest some way to work around  
> this problem.
> regards
> Rukmani Sridharan
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