[gmx-users] How to fix molecules in gromacs?
Daniele Veclani
danieleveclani at gmail.com
Mon Jul 18 11:34:25 CEST 2016
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?
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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list