Hi all!<br>I'm trying to run some energy minimization with gromacs 3.3.1 on a system that I have transformed from cg to aa. After the reverse transformation I solvate the system and I try to minimize just the proteins (my system is a dimer) keeping fixed the water. Then the idea would be to minimize the water keeping the protein in harmonic distance constraints as I just want to obtain an aa system which describes the configuration obtained previously in the cg representation.<br>
So, I first use genrestr to create the .itp file for fixing the position of the water, then I run 10 ps of EM and what I get is the following error message:<br><br>Stepsize too small, or no change in energy.<br>Converged to machine precision,<br>
but not to the requested precision Fmax < 10<br><br>Double precision normally gives you higher accuracy.<br>You might need to increase your constraint accuracy, or turn<br>off constraints alltogether (set constraints = none in mdp file)<br>
<br>From what I've read in previous posts the problem might be either in the mdp file or in the topology, but I don't understand what have I made wrong. Here is my mdp file<br><br> Lines starting with ';' ARE COMMENTS<br>
; Everything following ';' is also comment<br><br>title = Energy Minimization ; Title of run<br><br>; The following line tell the program the standard locations where to find certain files<br>cpp = /lib/cpp ; Preprocessor<br>
<br>; Define can be used to control processes<br>define = -DEPOSRES<br>;define = -DFLEXIBLE<br>; Parameters describing what to do, when to stop and what to save<br>integrator = steep ; Algorithm (steep = steepest descent minimization)<br>
emtol = 10.0 ; Stop minimization when the maximum force < 1.0 kJ/mol<br>dt = 0.005<br>;nsteps = 2000<br>nsteps = 5000 ; Maximum number of (minimization) steps to perform<br>
nstenergy = 1 ; Write energies to disk every nstenergy steps<br>energygrps = System ; Which energy group(s) to write to disk<br><br>; Parameters describing how to find the neighbors of each atom and how to calculate the interactions<br>
nstlist = 1 ; Frequency to update the neighbor list<br>ns_type = grid ; Method to determine neighbor list (simple, grid)<br>coulombtype = Reaction-Field ; Treatment of long range electrostatic interactions<br>
epsilon_rf = 78<br>rcoulomb = 1.4 ; long range electrostatic cut-off<br>rvdw = 1.4 ; long range Van der Waals cut-off<br>constraints = none ; Bond types to replace by constraints<br>
pbc = xyz ; Periodic Boundary Conditions (yes/no)<br><br>table-extension = 1.2<br><br>and this is my topology<br><br>;<br>; File 'dynamin_dimer_fg.top' was generated<br>; By user: vitalini (213883)<br>
; On host: goat<br>; At date: Mon Jan 30 11:02:21 2012<br>;<br>; This is your topology file<br>; "The Poodle Chews It" (F. Zappa)<br>;<br>; Include forcefield parameters<br>#include "/home/cocktail/vitalini/gromacs_special/share/gromacs/top/ffG53a6m.itp"<br>
<br>; Include chain topologies<br>#include "dynamin_dimer_fg_A.itp"<br>#include "dynamin_dimer_fg_B.itp"<br><br>; Include water topology<br>#include "/home/cocktail/vitalini/gromacs_special/share/gromacs/top/spc.itp"<br>
<br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>[ position_restraints ]<br>; i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>#endif<br><br><br>;Include restraints on water<br>
#ifdef POSRES_WAT<br>#include "posre_wat.itp"<br>#endif<br><br>; Include generic topology for ions<br>#include "/home/cocktail/vitalini/gromacs_special/share/gromacs/top/ions.itp"<br><br>[ system ]<br>
; Name<br>Protein in water<br><br>[ molecules ]<br>; Compound #mols<br>Protein_A 1<br>Protein_B 1<br>;SOL 390842<br>SOL 390820<br>NA+ 22<br><br>while this is the posre_wat.itp file I generated with genrestr<br clear="all">
<br>; position restraints for non-Protein of Protein in water<br><br>[ position_restraints ]<br>; i funct fcx fcy fcz<br>15231 1 1000 1000 1000<br>15232 1 1000 1000 1000<br>
15233 1 1000 1000 1000<br>15234 1 1000 1000 1000<br>15235 1 1000 1000 1000<br>15236 1 1000 1000 1000<br>15237 1 1000 1000 1000<br>
15238 1 1000 1000 1000<br>15239 1 1000 1000 1000<br>15240 1 1000 1000 1000<br>15241 1 1000 1000 1000<br>15242 1 1000 1000 1000<br>
15243 1 1000 1000 1000<br>15244 1 1000 1000 1000<br>15245 1 1000 1000 1000<br>15246 1 1000 1000 1000<br>15247 1 1000 1000 1000<br>
15248 1 1000 1000 1000<br>15249 1 1000 1000 1000<br>15250 1 1000 1000 1000<br>15251 1 1000 1000 1000<br>..........................<br>187712 1 1000 1000 1000<br>
<br>Any help?<br>Thanks Francesca<br><br><br>-- <br>Francesca Vitalini<br><br>PhD student at Computational Molecular Biology Group, <br>Department of Mathematics and Informatics, FU-Berlin<br>Arnimallee 6 14195 Berlin<br>
<br><a href="mailto:vitalini@zedat.fu-berlin.de" target="_blank">vitalini@zedat.fu-berlin.de</a><br><a href="mailto:francesca.vitalini@fu-berlin.de" target="_blank">francesca.vitalini@fu-berlin.de</a><br><br>+49 3083875776<br>
+49 3083875412<br><br>