[gmx-users] still dealing with GFP-like chromophore with LINCS warnings

2013-06-27 Thread Anna Marabotti

Dear gmx-users,
I'm still dealing with the problem of GFP-like chromophore. To be 
honest, with the help of another gmx user, I was able to obtain the 
topology of my chromophore, in protonated and unprotonated form, and I 
started performing the simulations. For the protonated chromophore, all 
worked well, and I obtained my simulations without many problems.


Instead, I'm experimenting problems with the protein containing the 
unprotonated form. In particular, when I started calculating the 
production run, using in the .mdp files exactly the same parameters used 
for the protonated form, I started obtaining a lot of LINCS warnings and 
production of a lot of stepX.pdb files. This happened only during 
the production run, whereas I have no errors during minimization and 
position-restrained dynamics. The minimization step seems to be OK and I 
did not further continue with it (I set emtol=500 and emstep=0.01; the 
result of minimization was:


Steepest Descents converged to Fmax  500 in 2114 steps

Potential Energy= -6.84833590617959e+05

Maximum force=4.57025361763790e+02 on atom 2129

Norm of force=9.42624640937790e+00

that seems pretty good for me.)

I tried to overcome the problem by using longer PR-MD (100 ps instead of 
10 for NVT; 1 ns instead of 100 ps for NPT) but it doesn't work, despite 
the fact that the energies and all other factors (temperature, pressure) 
are really stable during PR-MD. I also watched the trajectory using VMD 
but, apart from parts of protein crossing periodic boundaries (a thing 
that I see regularly in my simulations), I don't see anything strange 
(like system exploding). Apparently, it simply stops, and that's all.


Other things that trouble me are:
1) I checked the atoms with LINCS warning, and I see that not only those 
atoms belonging to chromophore are perturbed, but also other atoms in 
the backbone of the protein (mainly CA-C-N; many of them, but not all, 
are spatially close to chromophore).
2) during these production runs I also experimented many hardware 
problems (power outages) and software problems (bad job schedulation, 
problems in core communications etc) and I don't understand if these 
problems could affect the results of my simulation in this way. I ask 
this because my first production run was stopped because of a power 
outage, and in the .log file I saw a lot of errors very early; when the 
machine turned on, I resent exactly the same dynamics, and the errors 
were far later than before (in the first run, they came across 5 ns; in 
the second run not before 20 ns).
3) Last thing: when I started the production run, I switched the 
pressure coupling from Berendsen to Parrinello-Rahman (obviously not 
giving the .edr file to grompp for the creation of the full.tpr file) 
(on the contrary, the temperature coupling was left V-rescale both in 
PR-Md and production run). Can this switch perturb the system?


My question is: do I have to suppose that the unprotonated form of 
chromophore is badly parametrized, and this can influence all the rest 
of the protein in this way? If yes, why nothing happens when I do PR-MD? 
If not, do I have simply to perform a very very very long stabilization, 
do I have to perform a deeper minimization, do I have to avoid switching 
from Berendsen to Parrinello? What do you suggest me to do?


Thanks a lot
Anna

--
__
Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via Giovanni Paolo II, 132
84084 Fisciano (SA)
Italy
Phone: +39 089 969583
Fax: +39 089 969603
E-mail: amarabo...@unisa.it
Skype: annam1972
Web page: http://www.unisa.it/docenti/annamarabotti/index

Indifference is the eighth deadly sin (don Andrea Gallo)

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Re: [gmx-users] still dealing with GFP-like chromophore with LINCS warnings

2013-06-27 Thread Baptiste Demoulin
I did experience some troubles using Parrinello-Rahman after an
equilibration with Berendsen. Trying many different time-constant was the
solution ( I had to shift this constant from 10 ps for Berendsen to 5 ps
for PR). Did you try to change it ? I do not know the fundamental reasons
for this problem, though...

Baptiste


2013/6/27 Anna Marabotti amarabo...@unisa.it

 Dear gmx-users,
 I'm still dealing with the problem of GFP-like chromophore. To be honest,
 with the help of another gmx user, I was able to obtain the topology of my
 chromophore, in protonated and unprotonated form, and I started performing
 the simulations. For the protonated chromophore, all worked well, and I
 obtained my simulations without many problems.

 Instead, I'm experimenting problems with the protein containing the
 unprotonated form. In particular, when I started calculating the production
 run, using in the .mdp files exactly the same parameters used for the
 protonated form, I started obtaining a lot of LINCS warnings and production
 of a lot of stepX.pdb files. This happened only during the production
 run, whereas I have no errors during minimization and position-restrained
 dynamics. The minimization step seems to be OK and I did not further
 continue with it (I set emtol=500 and emstep=0.01; the result of
 minimization was:

 Steepest Descents converged to Fmax  500 in 2114 steps

 Potential Energy= -6.84833590617959e+05

 Maximum force=4.57025361763790e+02 on atom 2129

 Norm of force=9.42624640937790e+00

 that seems pretty good for me.)

 I tried to overcome the problem by using longer PR-MD (100 ps instead of
 10 for NVT; 1 ns instead of 100 ps for NPT) but it doesn't work, despite
 the fact that the energies and all other factors (temperature, pressure)
 are really stable during PR-MD. I also watched the trajectory using VMD
 but, apart from parts of protein crossing periodic boundaries (a thing that
 I see regularly in my simulations), I don't see anything strange (like
 system exploding). Apparently, it simply stops, and that's all.

 Other things that trouble me are:
 1) I checked the atoms with LINCS warning, and I see that not only those
 atoms belonging to chromophore are perturbed, but also other atoms in the
 backbone of the protein (mainly CA-C-N; many of them, but not all, are
 spatially close to chromophore).
 2) during these production runs I also experimented many hardware problems
 (power outages) and software problems (bad job schedulation, problems in
 core communications etc) and I don't understand if these problems could
 affect the results of my simulation in this way. I ask this because my
 first production run was stopped because of a power outage, and in the .log
 file I saw a lot of errors very early; when the machine turned on, I resent
 exactly the same dynamics, and the errors were far later than before (in
 the first run, they came across 5 ns; in the second run not before 20 ns).
 3) Last thing: when I started the production run, I switched the pressure
 coupling from Berendsen to Parrinello-Rahman (obviously not giving the .edr
 file to grompp for the creation of the full.tpr file) (on the contrary, the
 temperature coupling was left V-rescale both in PR-Md and production run).
 Can this switch perturb the system?

 My question is: do I have to suppose that the unprotonated form of
 chromophore is badly parametrized, and this can influence all the rest of
 the protein in this way? If yes, why nothing happens when I do PR-MD? If
 not, do I have simply to perform a very very very long stabilization, do I
 have to perform a deeper minimization, do I have to avoid switching from
 Berendsen to Parrinello? What do you suggest me to do?

 Thanks a lot
 Anna

 --
 __**
 Anna Marabotti, Ph.D.
 Assistant Professor
 Department of Chemistry and Biology
 University of Salerno
 Via Giovanni Paolo II, 132
 84084 Fisciano (SA)
 Italy
 Phone: +39 089 969583
 Fax: +39 089 969603
 E-mail: amarabo...@unisa.it
 Skype: annam1972
 Web page: 
 http://www.unisa.it/docenti/**annamarabotti/indexhttp://www.unisa.it/docenti/annamarabotti/index

 Indifference is the eighth deadly sin (don Andrea Gallo)

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