[gmx-users] How to fix molecules in gromacs?
Justin Lemkul
jalemkul at vt.edu
Mon Jul 18 11:49:49 CEST 2016
On 7/18/16 5:34 AM, Daniele Veclani wrote:
> Dear Justin
>
> Thanks for the answer.
>
> You can also give me an advice on this problem:
>
> I did as you told me. I used POSRES_0PCZ in .top file and -DPOSRES_0PCZ in
> .mdp file. But I find this error (grompp):
>
> "Atom index (1457) in position_restraints out of bounds (1456)"
>
> This is probably due to the fact that my posre.itp file is:
>
> ; position restraints for 0PCZ of cnt-cipro
>
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 43 1 1000 1000 1000
> 44 1 1000 1000 1000
> .
> .
> 1457 1 1000 1000 1000
> 1458 1 1000 1000 1000
> 1459 1 1000 1000 1000
> 1460 1 1000 1000 1000
> .
> .
> 1496 1 1000 1000 1000
> 1497 1 1000 1000 1000
> 1498 1 1000 1000 1000
>
> This file was built with genrestr.
>
> how can I solve this problem?
>
http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds
Also read the very detailed paragraph starting with "WARNING" in the genrestr
help information.
-Justin
>
> Best regards,
> D.V.
>
>
> 2016-07-17 15:21 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>
>>
>>
>> On 7/16/16 8:35 AM, Daniele Veclani wrote:
>>
>>> Dear gromacs users.
>>>
>>> I'm trying to fix a molecule inside the box. I want to use this molecule
>>> as
>>> an immobile reference in the pulling simulations.
>>>
>>> I can i do this? I have to use the position restraint or freezing Group?
>>>
>>> I tried to use position restraint, but, by analyzing the trajectories,
>>> I see that
>>> the molecule out of the box.
>>>
>>> This is my .top file:
>>> -----------------------------------
>>> ; Topology of CNT and CFX
>>> ;-----------------------------------
>>> #include "gromos54a7_atb.ff/forcefield.itp"
>>>
>>> ;-----------------------------------------------
>>> ; Uncomment the line with needed topology below
>>> ;-----------------------------------------------
>>> ; #include "zw"
>>>
>>> #include "cipro.itp"
>>>
>>> ; #include cnt
>>>
>>> #include "nano.itp"
>>> #ifdef DPOSRES_0PCZ
>>> #include "cnt-posre.itp"
>>> #endif
>>>
>>> #include "gromos54a7_atb.ff/spce.itp"
>>>
>>> [ system ]
>>> cnt-cipro
>>> [ molecules ]
>>> ; Compound nmols
>>> AUT8 1
>>> 0PCZ 1
>>> SOL 39030
>>>
>>> This is may .mdp file:
>>>
>>> ;preprocessing
>>> define = -DPOSRES_0PCZ
>>>
>>
>> Your syntax is wrong. The "-D" prefix needs to be added to whatever the
>> #ifdef keyword is. So for your topology to work, you need "define =
>> -DDPOSRES_0PCZ"
>>
>> Or, you can use -DPOSRES_0PCZ with #ifdef POSRES_0PCZ.
>>
>> You can check that no restraints are functioning by looking in the .log
>> file, as you will find no "Position Rest." energy term. If the restraints
>> are active, the associated energy is written.
>>
>> -Justin
>>
>>
>> ; Run control
>>> integrator = sd ; Langevin dynamics
>>> dt = 0.002
>>> nsteps = 300000 ; 0.6 ns
>>> nstcomm = 10
>>> ; Output control
>>> nstxout = 5000
>>> nstvout = 5000
>>> nstfout = 5000
>>> nstlog = 5000
>>> nstenergy = 5000
>>> nstxout-compressed = 5000
>>> ; Neighborsearching and short-range nonbonded interactions
>>> cutoff-scheme = verlet
>>> nstlist = 10
>>> ns_type = grid
>>> pbc = xyz
>>> rlist = 0.8
>>> ; Electrostatics
>>> coulombtype = PME
>>> rcoulomb = 1.2
>>> ; van der Waals
>>> vdwtype = cutoff
>>> rvdw = 1.2
>>> ; Apply long range dispersion corrections for Energy and Pressure
>>> DispCorr = EnerPres
>>> ; Spacing for the PME/PPPM FFT grid
>>> fourierspacing = 0.12
>>> ; EWALD/PME/PPPM parameters
>>> pme_order = 6
>>> ewald_rtol = 1e-06
>>> epsilon_surface = 0
>>> ; Temperature coupling
>>> ; tcoupl is implicitly handled by the sd integrator
>>> tcoupl = Nose-Hoover
>>> tc_grps = system
>>> tau_t = 1.0
>>> ref_t = 298.15
>>> ; Pressure coupling is on for pull
>>> Pcoupl = Parrinello-Rahman
>>> tau_p = 0.5
>>> compressibility = 4.5e-05
>>> ref_p = 1.0
>>> ; Free energy control stuff
>>> ; Generate velocities to start
>>> gen_vel = no
>>> gen_temp = 298.15
>>> gen_seed = -1
>>> ; options for bonds
>>> constraints = h-bonds ; we only have C-H bonds here
>>> ; Type of constraint algorithm
>>> constraint-algorithm = lincs
>>> ; Do not constrain the starting configuration
>>> continuation = yes
>>> ; Highest order in the expansion of the constraint coupling matrix
>>> lincs-order = 4
>>> lincs-iter = 1
>>> ; Pull code
>>> pull = umbrella
>>> pull_ngroups = 2
>>> pull_ncoords = 1
>>> pull_group1_name = AUT8
>>> pull_group2_name = 0PCZ
>>> pullgeometry = distance ; simple distance increase
>>> pull_coord1_groups = 1 2
>>> pull_dim = N Y N
>>> pull_coord1_rate = 0.01 ; 0.01 nm per ps = 10 nm per ns
>>> pull_coord1_k = 1000 ; kJ mol^-1 nm^-2
>>> pull_start = yes
>>>
>>> How can I fix this problem??
>>>
>>> I use gromacs 5.0.4
>>>
>>> Best regards
>>> D.V.
>>>
>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
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--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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