[gmx-users] LINCS warning during constrained md

[edesantis]

hi,

I've seen with vmd the gro file generated after the transformation, and 
after the 2 steps of minimization,
it seems that they have no problem,
while if I see the step_n.pdb file generated before the crash, there are 
some atoms far away from the rest of the protein, while this is not 
happening if I comment the restrains part


do you understand why??

thank you again,
Emiliano



On 2017-07-12 16:29, Mark Abraham wrote:
> Hi,
> 
> Those are all good things, but have you actually got out a molecular 
> viewer
> and looked at the input and output of your resolution conversion?
> 
> Mark
> 
> On Wed, Jul 12, 2017 at 4:25 PM edesantis <edesantis at roma2.infn.it> 
> wrote:
> 
>> Hi,
>> thanks for the prompt answer,
>> 
>> 
>> I've found the same problem even if I try to convert the coarse 
>> grained
>> pdb obtained from martinize.py, so in that case it should be not a
>> problem to have the conversion, for this reason I though it is a
>> methodological problem...
>> 
>> I've seen the blowing-up issues , but I think:
>> - the timestep is enough small  (0.0002)
>> -the system should be enough minimized via the previous steps (in fact
>> the sd converged to the machine precision in both cases, actually the
>> potential energy is ~10^5, but I don't know how to reduce it, I tried 
>> a
>> cg after the sd, but the proble is still there)
>> -there in not any pressure coupling
>> -I've tried a different temperature coupling (berensden, nose-hoover)
>> and it doesn't work
>> - the md stops at the first step, so there is not any .edr file 
>> produced
>> to be looked at
>> 
>> 
>> 
>> I don't know what else to do...
>> 
>> maybe, do you know another conversion protocol to use??
>> 
>> 
>> thank you again
>> Emiliano
>> 
>> On 2017-07-12 15:11, Mark Abraham wrote:
>> > Hi,
>> >
>> > Sounds like you might be
>> > http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the
>> > conversion doesn't work for your configuration. You should start by
>> > doing a
>> > visual check of the configuration for sanity, then follow the advice in
>> > that link.
>> >
>> > Mark
>> >
>> > On Wed, Jul 12, 2017 at 3:04 PM edesantis <edesantis at roma2.infn.it>
>> > wrote:
>> >
>> >> dear all,
>> >>
>> >> I am facing a problem with the conversion from Martini CG
>> >> representation
>> >> to All-atomistic one.
>> >>
>> >> I am using the initram.sh wrapper around the backward.py.
>> >>
>> >> There is a LINCS warning problem when the energy relaxation is
>> >> performed
>> >> using position restrained md
>> >> (I've also tried to run grompp and mdrun commands directly from the
>> >> terminal and the error persists, so it is not a wrapper problem).
>> >>
>> >> this is the .mdp file generated by the script:
>> >>
>> >> "define                   = -DPOSRES
>> >> integrator               = md
>> >> nsteps                   = 500
>> >> dt                       = 0.0002
>> >> pbc                      = xyz
>> >>
>> >> rcoulomb                 = 0.9
>> >> rlist                    = 0.9
>> >> rvdw                     = 0.9
>> >>
>> >> tcoupl                   = v-rescale
>> >> ref_t                    = 200
>> >> tau_t                    = 0.1
>> >> tc_grps                  = System
>> >>
>> >> gen_vel                  = yes
>> >> gen_temp                 = 300
>> >>
>> >> constraints              = all-bonds "
>> >>
>> >>
>> >> this is the error I found in the .log file:
>> >>
>> >> "Fatal error:
>> >> Too many LINCS warnings (1034)
>> >> If you know what you are doing you can adjust the lincs warning
>> >> threshold in your mdp file
>> >> or set the environment variable GMX_MAXCONSTRWARN to -1,
>> >> but normally it is better to fix the problem "
>> >>
>> >> I tired to comment the constrains part and all is working, but since
>> >> the
>> >> structure should not be altered too much, I think the constraints are
>> >> required (if I constrain only the h-bonds, it is also working).
>> >>
>> >> I've also added to the .mdp file the lines:
>> >> " lincs-order              = 4 (or 2 or 8)
>> >> lincs-iter               = 1 (or 2 or 10)
>> >> "
>> >> but it is still not working...
>> >>
>> >>
>> >> any of you have suggestions to solve the problem??
>> >> how is it possible to change the environment variable?
>> >>
>> >>
>> >> thanks in advance for your help
>> >> Emiliano
>> >>
>> >> --
>> >> Emiliano De Santis
>> >>
>> >> --
>> >> Gromacs Users mailing list
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>> 
>> --
>> Emiliano De Santis
>> --
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-- 
Emiliano De Santis