[gmx-users] Problem with Charmm in gromacs

[Justin A. Lemkul]

Fabrizio Marinelli wrote:
> Here it is my .mdp file, i attach you also the topology file, just to be
> more specific the one that are 0 are the SR interactions, thank you very
> much.

For diagnostic purposes, can you re-process your structure using a different 
force field and try again?  If the energies are still coming up zero, then there 
may be something wrong in the code as a whole, otherwise it is specific to the 
CHARMM force field.  Either way, I'm out of my league on this one :)  Maybe a 
developer can comment.

-Justin

> Fabrizio
> 
> title                    = Teaa MD
> cpp                      = /lib/cpp
> include                  =
> integrator               = md
> comm_mode                = Linear
> nstcomm                  = 10
> tinit                    = 0
> comm-grps                = System
> dt                       = 0.002
> nsteps                   = 6000000
> ; OUTPUT CONTROL OPTIONS =
> ; Output frequency for coords (x), velocities (v) and forces (f) =
> nstxout                  = 5000
> nstvout                  = 5000
> ; Output frequency for energies to log file and energy file =
> nstlog                   = 500
> nstenergy                = 500
> nstxtcout                = 500
> xtc-precision            = 100000
> xtc_grps                 = System
> energygrps               = System
> pbc                      = xyz
> nstlist                  = 5
> epsilon_r                = 1.
> ns_type                  = grid
> coulombtype              = pme
> vdwtype                  = Cut-Off
> fourierspacing           = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order                = 4
> ewald_rtol               = 2.2e-05
> epsilon_surface          = 0
> optimize_fft             = yes
> rlist                    = 1.2
> rcoulomb                 = 1.2
> rvdw                     = 1.2
> tcoupl                   = Berendsen
> tc-grps                  = System
> tau_t                    = 1.0
> ref_t                    = 298
> pcoupl                   = Berendsen
> pcoupltype               = isotropic
> tau_p                    = 2.5
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> ; Dielectric constant of reaction field =
> epsilon_rf               = 80.0
> gen_vel                  = yes
> gen_temp                 = 298
> gen_seed                 = 173529
> constraints              = all-bonds
> constraint_algorithm     = lincs
> shake_tol                = 0.0001
> ; Highest order in the expansion of the constraint coupling matrix =
> lincs-order              = 4
> ; Lincs will write a warning to the stderr if in one step a bond =
> ; rotates over more degrees than =
> lincs-warnangle          = 30
> user1-grps               = System
> ; Non-equilibrium MD stuff =
> acc-grps                 =
> accelerate               =
> freezegrps               =
> freezedim                =
> cos-acceleration         =
> 
> 
>>
>> Fabrizio Marinelli wrote:
>>> Hi all,
>>> I have downloaded the latest git version of gromacs (yesterday) in which
>>> it is possible to use the charmm27 force field, I constructed the
>>> topology
>>> for my protein using the pdb2gmx program, everything goes ok also with
>>> the
>>> solvation, but then when i run the MD i notice that coulomb and LJ
>>> interaction are 0 and also the protein consequently unfold.
>>> Did any of you found this kind of problem? Could some of you rpopose
>>> eventually a solution?
>> Can you post your .mdp file?
>>
>> -Justin
>>
>>> Thanks in advance,
>>> Fabrizio
>>>
>>>
>>> ----------------------------------------------------------------
>>>   SISSA Webmail https://webmail.sissa.it/
>>>   Powered by SquirrelMail http://www.squirrelmail.org/
>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
> 
> 
> 
> ----------------------------------------------------------------
>   SISSA Webmail https://webmail.sissa.it/
>   Powered by SquirrelMail http://www.squirrelmail.org/

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================