Dear Justin, I would like to know weather the parameters below are correct for NVT equilibiration whicle doig a simulation in vaccum ?
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 = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; 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 ns_type = simple ; search neighboring grid cells nstlist = 0 ; 10 fs rlist = 0.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.0 ; short-range electrostatic cutoff (in nm) rvdw = 0.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 0 ; cubic interpolation fourierspacing = 0.0 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Other ; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = no ; 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 Thank You *Anurag Dobhal* *Graduate Student (Bioprocess Technology)* *Institute of Chemical Technology, Mumbai* *Contact: +91 8898486877* On Thu, Feb 23, 2017 at 7:23 PM, Anurag Dobhal < anurag.dob...@nano-medicine.co.in> wrote: > Thank you ! > > > > > *Anurag Dobhal* > *Graduate Student (Bioprocess Technology)* > *Institute of Chemical Technology, Mumbai* > *Contact: +91 8898486877* > > > On Thu, Feb 23, 2017 at 7:09 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 2/23/17 8:29 AM, Anurag Dobhal wrote: >> >>> Thank you. Should I not use PME and PBC while performing simulations in >>> Vaccum ? >>> >>> >> No, you should not. Use no PBC and infinite cutoffs (all cutoffs set to >> zero) to mimic vacuum conditions. Otherwise you're simulating some type of >> diffusely occupied crystal environment. >> >> >> -Justin >> >> -- >> ================================================== >> >> 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 >> >> jalem...@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-requ...@gromacs.org. >> > > -- *DISCLAIMER:* *This communication is intended only for the person or entity to which it is addressed and may contain confidential and / or privileged material. Any review, retransmission, dissemination or other use is prohibited. If you have received this in error, please contact the sender and delete this material from your computer. Any comments or statements made herein do not necessarily reflect those of Nanomedicine Research Group. Before opening the email or accessing any attachments, please check and scan for virus.* -- 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-requ...@gromacs.org.