[gmx-users] LINCS warning during constrained md

Fri Jul 14 10:26:04 CEST 2017

Dear Mark,
I understand your point,
but I've used the Martini-backmapping protocol written in the initram.sh 
wrapper found in Martini documentation 
(https://github.com/Tsjerk/MartiniTools/blob/master/initram.sh), so it 
seems to me quite weird that it was not working in the proper manner.

an other problem is that I've to convert some thousands of structure 
extracted from the martini trajectory,
I thought that this kind of conversion doesn't require to much effort, 
so for this reason I thought that the posres flag was useful to limit 
the computational time... maybe I'm wrong

Can I avoid to use constrained bonds and use only posres? what do you 
think about?

in addition, for you, how many steps of md have I to perform to do this 
kind of equilibration? have I to look necessarily at the rmsd in each 
trajectory? I'd like to have a robust protocol to do all the conversions 
in an automatic way...

thank you again for your suggestions
regards,
Emiliano

On 2017-07-12 17:23, Mark Abraham wrote:
> Hi,
> 
> I would avoid using the combination of position restraints and 
> constrained
> bonds with an input structure that is not necessarily consistent with 
> the
> constraints. That's a recipe for large forces. I wouldn't use position
> restraints in such a process unless I had some reason to believe that 
> my
> starting structure was special *and* saw a large deformation if I 
> didn't
> use the restraints. If I saw the deformation, I would wonder why I 
> thought
> it was special.
> 
> If you're trying to relax a thing, let it relax. :-) If something 
> strange
> happens, consider that when it has happened. Obviously that means you 
> want
> to look at what happens when you did your equilibration, but you were 
> going
> to do that anyway. Right? ;-)
> 
> Mark
> 
> On Wed, Jul 12, 2017 at 5:17 PM edesantis <edesantis at roma2.infn.it> 
> wrote:
> 
>> 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
>> >> >>
>> >> >> --
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>> >>
>> >> --
>> >> Emiliano De Santis
>> >> --
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>> --
>> Emiliano De Santis
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-- 
Emiliano De Santis