[gmx-users] how to pull along Z direction
Lalita Shaki
lalitashaky at gmail.com
Wed Aug 20 17:44:28 CEST 2014
Hi Albert,
For pulling along the Z axis it is enough to align your system to
this axis (you can use editconf for that). You can then either use
the pull-geometry
= distanceand pull-dim = N N Yor you can use pull-geometry = direction
and pull-vec = 0 0 z=the distance between your pulling groups
Lalita
Hello:
I am going to calculate the PMF of a small molecule accross the lipids
bilyaers. I am just wondering how can we define the parameters along Z
direction?
thank you very much
ALbert
On Wed, Aug 20, 2014 at 12:00 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
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> 1. too many lincs warnings (Meenakshi Rajput)
> 2. how to pull along Z direction? (Albert)
> 3. delete molecule with command line? (Albert)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 20 Aug 2014 13:29:30 +0530
> From: Meenakshi Rajput <ashi.rajput39 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] too many lincs warnings
> Message-ID:
> <
> CAH5GTB+C8iuB7EM9sfLHX4nFA6PuuDfv-JUn9Q9NmxAbzgGW9w at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> hello users
> I had done energy minimisation of protein-ligand complex and i got negative
> potential. Also the ligand was at right place after EM run but when I tried
> the positional restrained run, too many lincs warnings came and md run
> stopped suddenly. I am using charmm force field and mdp file settings for
> position restrined run are:-
> define = -DPOSRES ; position restrain the protein
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 50000 ; 2 * 50000 = 100 ps
> dt = 0.002 ; 2 fs
> ; Output control
> nstxout = 500 ; save coordinates every 0.2 ps
> nstvout = 500 ; save velocities every 0.2 ps
> nstenergy = 500 ; save energies every 0.2 ps
> nstlog = 500 ; update log file every 0.2 ps
> ; Bond parameters
> continuation = yes ; first dynamics run
> constraint_algorithm = lincs ; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> cutoff-scheme = Verlet
> ns_type = grid ; search neighboring grid cells
> nstlist = 10 ; 10 fs
> rlist = 1.2 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
> rvdw-switch = 1.0
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range
> electrostatics
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.16 ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl = V-rescale ; modified Berendsen thermostat
> tc-grps = Protein Non-Protein ; two coupling groups - more
> accurate
> tau_t = 0.1 0.1 ; time constant, in ps
> ref_t = 300 300 ; reference temperature, one for each group,
> in K
> ; Pressure coupling is off
> pcoupl = no ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
> ; Dispersion correction
> DispCorr = EnerPres ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = yes ; assign velocities from Maxwell distribution
> gen_temp = 300 ; temperature for Maxwell distribution
> gen_seed = -1 ; generate a random seed
>
> Please tell me if there is something wrong with mdp settings or is it some
> other problem?
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 20 Aug 2014 10:17:39 +0200
> From: Albert <mailmd2011 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] how to pull along Z direction?
> Message-ID: <53F459A3.1070806 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello:
>
> I am going to calculate the PMF of a small molecule accross the lipids
> bilyaers. I am just wondering how can we define the parameters along Z
> direction?
>
> thank you very much
> ALbert
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 20 Aug 2014 11:27:31 +0200
> From: Albert <mailmd2011 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] delete molecule with command line?
> Message-ID: <53F46A03.1040901 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hello:
>
> I am just wondering is it possible to delet water molecules within 4A of
> a ligand through Gromacs command line? Everytime I have to do this in
> VMD which is a little bit complecated.....
>
> thank you very much.
> Albert
>
>
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> End of gromacs.org_gmx-users Digest, Vol 124, Issue 97
> ******************************************************
>
--
Lalita S. Uribe.
European Master in Theoretical Chemistry and Computational Modeling.
PhD student. Johannes Gutenberg-Universität Mainz
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