[gmx-users] LINCS warning during constrained md

[edesantis]

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