On 29/02/2012 9:26 PM, Steven Neumann wrote:
On Tue, Feb 28, 2012 at 10:50 PM, Justin A. Lemkul <[email protected] <mailto:[email protected]>> wrote:Steven Neumann wrote: On Tue, Feb 28, 2012 at 6:33 PM, Justin A. Lemkul <[email protected] <mailto:[email protected]> <mailto:[email protected] <mailto:[email protected]>>> wrote: Steven Neumann wrote: I run energy minimization of my protein with implicit solvent: constraints = none integrator = steep dt = 0.001 ; ps nsteps = 30000 vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb = 0 rvdw = 0 comm-mode = angular comm-grps = Protein optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 5.0 emstep = 0.01 ; ; Implicit solvent ; implicit_solvent = GBSA gb_algorithm = OBC nstgbradii = 1 rgbradii = 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm = Ace-approximation sa_surface_tension = 2.25936 And I obtained: Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 30000 Step Time Lambda 0 0.00000 0.00000 Steepest Descents converged to Fmax < 1000 in 1 steps Potential Energy = inf Maximum force = 0.0000000e+00 on atom 0 Norm of force = nan Can you please explain? Not without more information. 1. What is in the system? - protein without specified box 2. Which version of Gromacs is this? - Gromacs 4.5.4 3. Are you using GPU or CPU architecture? - I run it straight from the cluster on a specific node Doesn't answer the question, but I'll assume CPU since EM doesn't work on GPU's. Just checking. 4. Does an in vacuo minimization work (i.e., just turn off the GB parts)? - yes, it works And what is the output? In any case, I can't reproduce any problem doing EM with implicit solvent in 4.5.4 - my test systems work quite well. It may just be that the system cannot be minimized because of some clash that is unfavorable in an implicit solvent environment (thus causing an immediate halt, though that would be odd) but can be resolved in vacuo. Try using the structure produced by in vacuo minimization as input into the implicit solvent EM to see if this may be the case. What shoould be the value for emtol in implicit solvent model with protein with app. 150 residues? One that is sufficient for the inherent forces in the system and for your application ;) I don't think there are any hard and fast rules here for standard MD, and the target is not dictated by the size of the protein. -Justin Thank you Justin.Mark, would you suggest equilibration e.g. for 1ns with no restraints and no constraints in implicic solvent with timestep =0.0005 and then run MD with implicit employing LINCS?
I have suggested such equilibration protocols in the past for implicit solvent - maybe 1ns is excessive. I've had simple peptide systems with no atomic clashes that have wanted such gentle treatment.
Mark
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