Re: [gmx-users] large forces and monstrous water molecules in energy minimization step
Hi, For the dynamics to work you indeed need smaller forces (on the order of 10^3 in GMX units). Using flexible water molecules I was able to get this for your NaCl model. Just add: define = -DFLEXIBLE To your input. This should work also to fill in the voids I guess. Ran -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- Justin A. Lemkul wrote: > > Use a different box size. I replicated your problem, but your run > completes successfully with a box set up with editconf -d 1 instead of > -d 3.3. > > If you set nstxout = 1 during the EM process, you'll see the > problematic water molecule become unstable. It looks as if there is a > small void in the solvent (due to the way genbox tries to stack > solvent configurations) and your water molecule simply can't find a > good orientation within that void. > > -Justin > > Ehud Schreiber wrote: >> Dear GROMACS users, >> >> >> >> When trying to simulate a pair of interacting proteins in water, I >> have encountered problems that ultimately resulted in the simulation >> crashing. I then tried to simplify the system as far as possible >> while retaining the problem; I now believe the problem (or at least a >> part of it) lies in the energy minimization step (the first molecular >> dynamics one). Specifically, the forces encountered during this step >> are very large, and some water molecules (which are supposed to be >> rigid) become giant and misshapen. >> >> >> >> In more details: >> >> 1) I use GROMACS version 4.0.7, single precision, on a server with >> two Intel x86-64 processors and the redhat 5.4 linux OS. >> >> 2) I created a PDB file, called NaCl.pdb, with only two “atoms”, >> actually Na+ and Cl- ions separated by their distance in the lattice >> of salt: >> >> >> >> HET NA A 1 1 >> >> HET CL A 1 1 >> >> HETNAM NA SODIUM ION >> >> HETNAM CL CHLORIDE ION >> >> FORMUL 1 NANA 1+ >> >> FORMUL 2 CLCL 1- >> >> HETATM1 NANA A 1 -1.410.0 0.01.00 >> 0.0 NA >> >> HETATM2 CLCL A 1 +1.410.0 0.01.00 >> 0.0 CL >> >> >> >> 3) I use the tip3p water model: >> >> >> >> pdb2gmx -f NaCl.pdb -water tip3p >> >> >> >> 4) I create the box: >> >> >> >> editconf -f conf.gro -bt dodecahedron -d 3.3 -o box.gro >> >> >> >> 5) I add water using spc216, creating the saltwater.gro file (which >> seems O.K. by inspection): >> >> >> >> genbox -cp box.gro -cs spc216.gro -p topol.top -o saltwater.gro >> >> >> >> 6) I create the energy minimization parameter file em.mdp: >> >> >> >> --em.mdp-- >> >> integrator = steep >> >> nsteps = 200 >> >> nstlist = 10 >> >> rlist = 1.0 >> >> coulombtype = pme >> >> rcoulomb= 1.0 >> >> vdwtype = Cut-off >> >> rvdw= 1.0 >> >> nstenergy = 10 >> >> -- >> >> >> >> 7) I prepare the em.tpr file for the energy minimization run: >> >> >> >> grompp -f em.mdp -p topol.top -c saltwater.gro -o em.tpr >> >> >> >> 8) I run the energy minimization step: >> >> >> >> mdrun -v -deffnm em >> >> >> >> 9) Looking at the em.log file I see that this step converged to >> machine precision but did not have maximal force < 10: >> >> >> >> … >> >> Enabling SPC water optimization for 7561 molecules. >> >> … >> >> Max number of connections per atom is 2 >> >> Total number of connections is 30244 >> >> Max number of graph edges per atom is 2 >> >> Total number of graph edges is 30244 >> >> Going to use C-settle (7561 waters) >> >> wo = 0.33, wh =0.33, wohh = 3, rc = 0.075695, ra = 0.0390588 >> >> rb = 0.0195294, rc2 = 0.15139, rone = 1, dHH = 0.15139, dOH = 0.09572 >> >> … >> >> Stepsize too small, or no change in energy. >> >> Converged to machine precision, >> >> but not to the requested precision Fmax < 10 >> >> … >> >> Steepest Descents converged to machine precision in 36 steps, >> >> but did not reach the requested Fmax < 10. >> >> Potential Energy = -3.4678925e+05 >> >> Maximum force = 6.4623531e+05 on atom 11052 >> >> Norm of force = 5.4643726e+03 >> >> >> >> 10) Looking at the em.gro file I see one monstrous water molecule >> (no. 3686); e.g., it has |HW2-OW| = 3.384876 nm, while the normal >> distance is about 0.1 nm. Its HW2 atom (no. 11054) is close to >> another water molecule (no. 5849), e.g., 0.047 nm from the latter’s >> HW2 atom (no. 17543): >> >> >> >> … >> >> 3686SOL OW11052 4.348 3.778 -0.629 >> >> 3686SOLHW111053 5.360 2.601 0.505 >> >> 3686SOLHW211054 6.518 1.650 0.861 >> … >> >> 5849SOL OW17541 6.525 1.698 0.900 >> >> 5849
Re: [gmx-users] large forces and monstrous water molecules in energy minimization step
Use a different box size. I replicated your problem, but your run completes successfully with a box set up with editconf -d 1 instead of -d 3.3. If you set nstxout = 1 during the EM process, you'll see the problematic water molecule become unstable. It looks as if there is a small void in the solvent (due to the way genbox tries to stack solvent configurations) and your water molecule simply can't find a good orientation within that void. -Justin Ehud Schreiber wrote: Dear GROMACS users, When trying to simulate a pair of interacting proteins in water, I have encountered problems that ultimately resulted in the simulation crashing. I then tried to simplify the system as far as possible while retaining the problem; I now believe the problem (or at least a part of it) lies in the energy minimization step (the first molecular dynamics one). Specifically, the forces encountered during this step are very large, and some water molecules (which are supposed to be rigid) become giant and misshapen. In more details: 1) I use GROMACS version 4.0.7, single precision, on a server with two Intel x86-64 processors and the redhat 5.4 linux OS. 2) I created a PDB file, called NaCl.pdb, with only two “atoms”, actually Na+ and Cl- ions separated by their distance in the lattice of salt: HET NA A 1 1 HET CL A 1 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 1 NANA 1+ FORMUL 2 CLCL 1- HETATM1 NANA A 1 -1.410.0 0.01.00 0.0 NA HETATM2 CLCL A 1 +1.410.0 0.01.00 0.0 CL 3) I use the tip3p water model: pdb2gmx -f NaCl.pdb -water tip3p 4) I create the box: editconf -f conf.gro -bt dodecahedron -d 3.3 -o box.gro 5) I add water using spc216, creating the saltwater.gro file (which seems O.K. by inspection): genbox -cp box.gro -cs spc216.gro -p topol.top -o saltwater.gro 6) I create the energy minimization parameter file em.mdp: --em.mdp-- integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb= 1.0 vdwtype = Cut-off rvdw= 1.0 nstenergy = 10 -- 7) I prepare the em.tpr file for the energy minimization run: grompp -f em.mdp -p topol.top -c saltwater.gro -o em.tpr 8) I run the energy minimization step: mdrun -v -deffnm em 9) Looking at the em.log file I see that this step converged to machine precision but did not have maximal force < 10: … Enabling SPC water optimization for 7561 molecules. … Max number of connections per atom is 2 Total number of connections is 30244 Max number of graph edges per atom is 2 Total number of graph edges is 30244 Going to use C-settle (7561 waters) wo = 0.33, wh =0.33, wohh = 3, rc = 0.075695, ra = 0.0390588 rb = 0.0195294, rc2 = 0.15139, rone = 1, dHH = 0.15139, dOH = 0.09572 … Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 … Steepest Descents converged to machine precision in 36 steps, but did not reach the requested Fmax < 10. Potential Energy = -3.4678925e+05 Maximum force = 6.4623531e+05 on atom 11052 Norm of force = 5.4643726e+03 10) Looking at the em.gro file I see one monstrous water molecule (no. 3686); e.g., it has |HW2-OW| = 3.384876 nm, while the normal distance is about 0.1 nm. Its HW2 atom (no. 11054) is close to another water molecule (no. 5849), e.g., 0.047 nm from the latter’s HW2 atom (no. 17543): … 3686SOL OW11052 4.348 3.778 -0.629 3686SOLHW111053 5.360 2.601 0.505 3686SOLHW211054 6.518 1.650 0.861 … 5849SOL OW17541 6.525 1.698 0.900 5849SOLHW117542 6.606 1.649 0.918 5849SOLHW217543 6.481 1.648 0.832 … 11) During the simulation, several files called stepnnl.pdb were produced for problematic steps, where nn=11,15,19 and l=b,c. For example, the file step19c.pdb indeed shows a problematic water molecule no. 3686, while step19b.pdb does not. Likewise, the earlier step11c.pdb shows a problematic water molecule no. 3266 while step11b.pdb seems proper. The stdout/stderr of mdrun contains warnings like the following: … t = 0.019 ps: Water molecule starting at atom 11052 can not be settled. Check for bad contacts and/or reduce the timestep. … 12) Reducing the neighbor list update time, i.e., setting nstlist = 1, does not produce any change. 13) Trying to use the conjugate gradient integrator instead of steepest descent, i.e., setting integrator = cg, is even worse - the running crashes: … Step 16, Epot=-1.258771e+35, Fnorm= nan, Fmax= inf (atom 14493) Segmentation fault Exit 139 So, am I doing something wrong? How can I avoid these problems? Thanks, Ehud Schreiber.
[gmx-users] large forces and monstrous water molecules in energy minimization step
Dear GROMACS users, When trying to simulate a pair of interacting proteins in water, I have encountered problems that ultimately resulted in the simulation crashing. I then tried to simplify the system as far as possible while retaining the problem; I now believe the problem (or at least a part of it) lies in the energy minimization step (the first molecular dynamics one). Specifically, the forces encountered during this step are very large, and some water molecules (which are supposed to be rigid) become giant and misshapen. In more details: 1) I use GROMACS version 4.0.7, single precision, on a server with two Intel x86-64 processors and the redhat 5.4 linux OS. 2) I created a PDB file, called NaCl.pdb, with only two "atoms", actually Na+ and Cl- ions separated by their distance in the lattice of salt: HET NA A 1 1 HET CL A 1 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 1 NANA 1+ FORMUL 2 CLCL 1- HETATM1 NANA A 1 -1.410.0 0.01.00 0.0 NA HETATM2 CLCL A 1 +1.410.0 0.01.00 0.0 CL 3) I use the tip3p water model: pdb2gmx -f NaCl.pdb -water tip3p 4) I create the box: editconf -f conf.gro -bt dodecahedron -d 3.3 -o box.gro 5) I add water using spc216, creating the saltwater.gro file (which seems O.K. by inspection): genbox -cp box.gro -cs spc216.gro -p topol.top -o saltwater.gro 6) I create the energy minimization parameter file em.mdp: --em.mdp-- integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb= 1.0 vdwtype = Cut-off rvdw= 1.0 nstenergy = 10 -- 7) I prepare the em.tpr file for the energy minimization run: grompp -f em.mdp -p topol.top -c saltwater.gro -o em.tpr 8) I run the energy minimization step: mdrun -v -deffnm em 9) Looking at the em.log file I see that this step converged to machine precision but did not have maximal force < 10: ... Enabling SPC water optimization for 7561 molecules. ... Max number of connections per atom is 2 Total number of connections is 30244 Max number of graph edges per atom is 2 Total number of graph edges is 30244 Going to use C-settle (7561 waters) wo = 0.33, wh =0.33, wohh = 3, rc = 0.075695, ra = 0.0390588 rb = 0.0195294, rc2 = 0.15139, rone = 1, dHH = 0.15139, dOH = 0.09572 ... Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 ... Steepest Descents converged to machine precision in 36 steps, but did not reach the requested Fmax < 10. Potential Energy = -3.4678925e+05 Maximum force = 6.4623531e+05 on atom 11052 Norm of force = 5.4643726e+03 10) Looking at the em.gro file I see one monstrous water molecule (no. 3686); e.g., it has |HW2-OW| = 3.384876 nm, while the normal distance is about 0.1 nm. Its HW2 atom (no. 11054) is close to another water molecule (no. 5849), e.g., 0.047 nm from the latter's HW2 atom (no. 17543): ... 3686SOL OW11052 4.348 3.778 -0.629 3686SOLHW111053 5.360 2.601 0.505 3686SOLHW211054 6.518 1.650 0.861 ... 5849SOL OW17541 6.525 1.698 0.900 5849SOLHW117542 6.606 1.649 0.918 5849SOLHW217543 6.481 1.648 0.832 ... 11) During the simulation, several files called stepnnl.pdb were produced for problematic steps, where nn=11,15,19 and l=b,c. For example, the file step19c.pdb indeed shows a problematic water molecule no. 3686, while step19b.pdb does not. Likewise, the earlier step11c.pdb shows a problematic water molecule no. 3266 while step11b.pdb seems proper. The stdout/stderr of mdrun contains warnings like the following: ... t = 0.019 ps: Water molecule starting at atom 11052 can not be settled. Check for bad contacts and/or reduce the timestep. ... 12) Reducing the neighbor list update time, i.e., setting nstlist = 1, does not produce any change. 13) Trying to use the conjugate gradient integrator instead of steepest descent, i.e., setting integrator = cg, is even worse - the running crashes: ... Step 16, Epot=-1.258771e+35, Fnorm= nan, Fmax= inf (atom 14493) Segmentation fault Exit 139 So, am I doing something wrong? How can I avoid these problems? Thanks, Ehud Schreiber. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
