I am no expert in implicit solvent simulations but I think for these simulations it is better to use stochastic dynamic integrators with no pbc (instead of NVT) and infinite (or very large) cut-off distances because there is no actual water molecule in your simulation box and [normally] you do not have to worry about the boundary effects.
For finding appropriate parameters, you should have a look at the Gromacs manual and read the literature but if you need a quick example see below (please note that this is just an example). Cheers, Saber ; RUN CONTROL PARAMETERS integrator = sd tinit = 0 ; Starting time dt = 0.002 ; 2 femtosecond time step for integration nsteps = 50000 ; OUTPUT CONTROL OPTIONS nstxout = 50000 ; Writing full precision coordinates every nanosecond nstvout = 50000 ; Writing velocities every nanosecond nstfout = 0 ; Not writing forces nstlog = 2500 ; Writing to the log file every step nstenergy = 2500 ; Writing out energy information every step nstxtcout = 2500 ; Writing coordinates every 5 ps energygrps = System ; NEIGHBORSEARCHING PARAMETERS nstlist = 0 ns-type = simple pbc = no rlist = 0 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = cut-off rvdw = 0 rcoulomb = 0 ; Temperature coupling tc-grps = System tau_t = 10 ref_t = 300 ld_seed = 123 ;implicit solvent implicit_solvent = GBSA gb_algorithm = OBC rgbradii = 0 gb_epsilon_solvent = 80 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen_temp = 300 comm_mode = Angular ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = yes lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 On 17 October 2012 17:51, Albert <[email protected]> wrote: > Hi Saber: > > thanks a lot for such kind reply. > How about the second question? I don't find any tutorial for the GBSA > solvent simulation in Gromacs website and I am not sure what kind of > parameters we should use for GBSA. > > > thank you very much > best > Albert > > On 10/17/2012 05:48 PM, saber naderi wrote: > >> Hi Albert, >> >> Regarding you first question, your protein is relatively big and in my >> opinion 28 replicas is not much for a protein made of 290 AA with the >> temperature range of 280-530. One thing that you can do is to use a lower >> value for exchange probability to have less replicas. By doing this the >> average time interval between exchanges becomes longer (assuming that you >> keep the exchange attempt interval fixed). This is not necessarily a bad >> thing because in case of large proteins the dynamics is slow anyway and it >> is useful if you let the system relax between exchanges. >> >> Cheers, >> Saber >> >> On 17 October 2012 17:32, Albert <[email protected]> wrote: >> >> hello: >>> >>> I am going to perform replica exchange MD with Gromacs and I found some >>> problems there: >>> >>> 1. my protein have around 290 aa with 4680 atoms. If I would like to >>> perform with implicite solvent with exchange probability 0.2, I found >>> from >>> http://folding.bmc.uu.se/remd/ that I will have to generate around 28 >>> different replica between 280 and 530. However, I seldom see someone >>> perform so much round of replicas......If I perform with explicit solvent >>> with 8000 water molecules, the number of replica goes up to 112.... That' >>> unbelievable a lot. My protein is a normal size and when we read the >>> paper, >>> usually people will produce no more than 12 replica. Why it is so much >>> round for my case? >>> >>> 2. If I would like to perform in NVT with implicit solvent, shall I >>> change >>> something in the .mdp file? If the following (from Justine's tutorial) >>> all >>> right for the GBSA solvent? >>> >>> title = Protein-ligand complex NVT equilibration >>> define = -DPOSRES ; position restrain the protein and ligand >>> ; 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 >>> energygrps = Protein JZ4 >>> ; 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 = grid ; search neighboring grid cells >>> nstlist = 5 ; 10 fs >>> rlist = 0.9 ; short-range neighborlist cutoff (in nm) >>> rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) >>> rvdw = 1.4 ; short-range van der Waals cutoff (in nm) >>> ; Electrostatics >>> coulombtype = PME ; Particle Mesh Ewald for long-range >>> electrostatics >>> pme_order = 4 ; cubic interpolation >>> fourierspacing = 0.16 ; grid spacing for FFT >>> ; Temperature coupling >>> tcoupl = V-rescale ; modified Berendsen >>> thermostat >>> tc-grps = Protein_JZ4 Water_and_ions ; 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 >>> 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 >>> >>> >>> thank you very much >>> best >>> Albert >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> > >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>> posting! >>> >>> * Please don't post (un)subscribe requests to the list. 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