[gmx-users] Problem with Charmm in gromacs

[Pär Bjelkmar]

Hi Fabrizio,

Could you send me the input files and I'll take a look at it. You can send it to bjelkmar at cbr.su.se

Regards,
Pär Bjelkmar

29 apr 2010 kl. 16.34 skrev gmx-users-request at gromacs.org:

> Message: 3
> Date: Thu, 29 Apr 2010 10:33:53 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Problem with Charmm in gromacs
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Message-ID: <4BD998D1.6010405 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
> 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
>>> 

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