[gmx-users] gromacs.org_gmx-users Digest, Vol 172, Issue 89
sagar bathla
sagarbathla4 at gmail.com
Wed Aug 29 13:14:42 CEST 2018
hi Dan,
I got the warnings at the start of the mdrun.
Regards
Sagar
On Wed, Aug 29, 2018 at 3:30 PM <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. free energy of complex system (abhisek Mondal)
> 2. restrain ligand in free energy. (T?ng Ho?ng)
> 3. Re: rotation of atoms by more than 90 degrees & LINCS
> Warnings (Dan Gil)
> 4. Re: rotation of atoms by more than 90 degrees & LINCS
> Warnings (Dan Gil)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 29 Aug 2018 11:23:16 +0530
> From: abhisek Mondal <abhisek.mndl at gmail.com>
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] free energy of complex system
> Message-ID:
> <CA+DemH-XhcuMrUQa7yXXbV6E=
> f3+uLYYkPN2Zi3xg38dCTmRvQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
> I'm just trying to calculate free energy of a complex system using
> following method:
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html
>
> However, I'm facing some difficulties understanding how can I achieve the
> goal. The tutorial goes on with a single entity from lambda=0 to 1 with
> 0.05 spacing for data collection.
>
> Now, if I would like to calculate free energy of a complex (say, dimeric
> protein) then how am I supposed to design the lambda states ?
> I mean will it be like, one monomer will remain constant and the other
> monomer goes from lambda=0 to 1 state ? If that be the case then please
> suggest a way to customize the procedure.
>
> Please provide some suggestions.
> I'm really willing to apply this method in my scenario.
> Thank you.
> --
> Abhisek Mondal
>
> *Senior Research Fellow*
> *Protein Crystallography Group*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 29 Aug 2018 14:06:31 +0700
> From: T?ng Ho?ng <hoangtung9597 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] restrain ligand in free energy.
> Message-ID:
> <
> CAFn5Yuf4MYt_Q-XFN5qKdavN25OoUj4SRW-bELE21grnOyKzpQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello everyone,
> i am trying to calculate free energy for complex protein-ligand. but in
> tutorial it just have methane in water. So i find this
> http://www.alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016
> but the problem is i don know how to restrain this ligand.
> in file complex.top i see that intramolecular - interaction , bond, angle ,
> diheral. and in .mdp file i see bonds_lambda increase. I wonder how i can
> restrain like this . where i can find intramolecular -interaction/....
> Thank you for your help.
>
> Regrads,
> Tung,
>
> --
> Ho?ng T?ng / student
> hoangtung9597 at gmail.com / +(84) 0928 478 789
>
> University of Medicine and Pharmacy I Ho Chi Minh City
> 197 Nguyen Thai Hoc, Pham Ngu Lao, District 1, HCM City
> <https://htmlsig.com/signatures/0001DP594H>
>
> [image: Facebook] <https://htmlsig.com/t/000001DK2V24> [image: Skype]
> <https://htmlsig.com/t/000001DH4S28>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 29 Aug 2018 05:56:14 -0400
> From: Dan Gil <dan.gil9973 at gmail.com>
> To: gmx-users at gromacs.org
> Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] rotation of atoms by more than 90 degrees &
> LINCS Warnings
> Message-ID:
> <CAHMQ-OYTxnjHPnLzhU5C6X9YKQ-9aYUzTjqLz5Ksf+U=
> hoG30Q at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Sagar,
>
> At which time step do you get LINCS warnings?
>
> Also, please see:
> http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
>
> Dan
>
> On Tue, Aug 28, 2018 at 3:19 AM sagar bathla <sagarbathla4 at gmail.com>
> wrote:
>
> > Dear all,
> >
> > My system consists of 2 orthorhombic parallel graphene sheets in a big
> > triclinic box filled with water. when i am trying to run equillibration
> > then i am getting too many lincs warnings and simulation has been getting
> > crashed everytime. i have put retraint on all atoms of graphene but still
> > this problem is occuring again.
> >
> > My .mdp file looks like this
> > title = OPLS Graphene IN WATER NVT equilibration
> > define = -DPOSRES -DFLEXIBLE ; position restrain the protein
> >
> > ; Run parameters
> > integrator = md ; leap-frog integrator
> > nsteps = 500000 ; 2 * 500000 = 1000 ps
> >
> > dt = 0.002 ; 2 fs
> >
> > ; Output control
> > nstxout = 1000 ; save coordinates every 1.0 ps
> > nstvout = 1000 ; save velocities every 1.0 ps
> > nstenergy = 1000 ; save energies every 1.0 ps
> > nstlog = 1000 ; update log file every 1.0 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
> > lincs-warnangle = 90
> >
> > ; Neighborsearching
> > vdw-modifier = Force-switch
> > cutoff-scheme = Verlet
> > ns_type = grid ; search neighboring grid cells
> > nstlist = 10 ; 20 fs, largely irrelevant with
> > Verlet
> > rcoulomb = 1.2 ; short-range electrostatic
> cutoff
> > (in nm)
> > rvdw = 1.2
> > rlist = 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 = nose-hoover ; nose-hoover thermostat
> > tc-grps = GRA SOL ; 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
> > periodic-molecules = yes
> >
> > ; Dispersion correction
> > DispCorr = EnerPres ; account for cut-off vdW scheme
> >
> > ; number of steps for center of mass motion removal =
> > comm-mode = Linear
> > nstcomm = 1
> > comm-grps = GRA SOL
> > ; Velocity generation
> > gen_vel = no ; assign velocities from Maxwell
> > distribution
> > gen_temp = 300 ; temperature for Maxwell distribution
> > gen_seed = -1 ; generate a random seed
> >
> > ;non equillibrium md
> > freezegrps: GRA
> > freezedim: Y Y Y
> > i have tried various things but nothing is working.
> > please help to solve this problem
> >
> > Regards
> > Sagar Bathla
> > --
> > 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.
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 29 Aug 2018 05:56:14 -0400
> From: Dan Gil <dan.gil9973 at gmail.com>
> To: gmx-users at gromacs.org
> Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] rotation of atoms by more than 90 degrees &
> LINCS Warnings
> Message-ID:
> <CAHMQ-OYTxnjHPnLzhU5C6X9YKQ-9aYUzTjqLz5Ksf+U=
> hoG30Q at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Sagar,
>
> At which time step do you get LINCS warnings?
>
> Also, please see:
> http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
>
> Dan
>
> On Tue, Aug 28, 2018 at 3:19 AM sagar bathla <sagarbathla4 at gmail.com>
> wrote:
>
> > Dear all,
> >
> > My system consists of 2 orthorhombic parallel graphene sheets in a big
> > triclinic box filled with water. when i am trying to run equillibration
> > then i am getting too many lincs warnings and simulation has been getting
> > crashed everytime. i have put retraint on all atoms of graphene but still
> > this problem is occuring again.
> >
> > My .mdp file looks like this
> > title = OPLS Graphene IN WATER NVT equilibration
> > define = -DPOSRES -DFLEXIBLE ; position restrain the protein
> >
> > ; Run parameters
> > integrator = md ; leap-frog integrator
> > nsteps = 500000 ; 2 * 500000 = 1000 ps
> >
> > dt = 0.002 ; 2 fs
> >
> > ; Output control
> > nstxout = 1000 ; save coordinates every 1.0 ps
> > nstvout = 1000 ; save velocities every 1.0 ps
> > nstenergy = 1000 ; save energies every 1.0 ps
> > nstlog = 1000 ; update log file every 1.0 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
> > lincs-warnangle = 90
> >
> > ; Neighborsearching
> > vdw-modifier = Force-switch
> > cutoff-scheme = Verlet
> > ns_type = grid ; search neighboring grid cells
> > nstlist = 10 ; 20 fs, largely irrelevant with
> > Verlet
> > rcoulomb = 1.2 ; short-range electrostatic
> cutoff
> > (in nm)
> > rvdw = 1.2
> > rlist = 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 = nose-hoover ; nose-hoover thermostat
> > tc-grps = GRA SOL ; 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
> > periodic-molecules = yes
> >
> > ; Dispersion correction
> > DispCorr = EnerPres ; account for cut-off vdW scheme
> >
> > ; number of steps for center of mass motion removal =
> > comm-mode = Linear
> > nstcomm = 1
> > comm-grps = GRA SOL
> > ; Velocity generation
> > gen_vel = no ; assign velocities from Maxwell
> > distribution
> > gen_temp = 300 ; temperature for Maxwell distribution
> > gen_seed = -1 ; generate a random seed
> >
> > ;non equillibrium md
> > freezegrps: GRA
> > freezedim: Y Y Y
> > i have tried various things but nothing is working.
> > please help to solve this problem
> >
> > Regards
> > Sagar Bathla
> > --
> > 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.
> >
>
>
> ------------------------------
>
> --
> 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
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>
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