Re: [gmx-users] Freeze backbone & Pressure scaling more than 1%
이진희 wrote: > > > Dear all > > > > When I run produnction run using freeze backbone in GROMACS 4.0.5, the > error was shown. > > But I didn't use freeze backboone, the error wasn't shown. > > > > Step 1 Warning: Pressure scaling more than 1%. > > > > I changed "tau_p" value from 0.5 to 5 in md.mdp file, but the above > error was shown. > > I don't know how to solve it. Any one give some advice. Provide a full description. What's the system, how big is it, how did you equilibrate it, why/how are you freezing the backbone, does the run finish, does the trajectory look ok? Mark -- 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
Re: [gmx-users] typo in ffoplsaanb.itp for opls_179 (OS) and opls_180 (OS)
Pradip Biswas wrote: Hi, The atomic numbers of the atom types opls_179 (OS) and opls_180 (OS) are typed in as 7 in ffoplsaanb.itp instead of 8. Accordingly, while doing QMMM, these oxygen atoms are being recognized as Nitrogen atoms. DvdS fixed this in the git source earlier this week. Mark -- 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
[gmx-users] typo in ffoplsaanb.itp for opls_179 (OS) and opls_180 (OS)
Hi, The atomic numbers of the atom types opls_179 (OS) and opls_180 (OS) are typed in as 7 in ffoplsaanb.itp instead of 8. Accordingly, while doing QMMM, these oxygen atoms are being recognized as Nitrogen atoms. Biswas. -- 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
[gmx-users] freeze backbone & Pressure scaling error
Dear all When I run produnction run using freeze backbone in GROMACS 4.0.5, the error was shown. But I didn't use freeze backboone, the error wasn't shown. Step 1 Warning: Pressure scaling more than 1%. I changed "tau_p" value from 0.5 to 5 in md.mdp file, but the above error was shown. I don't know how to solve it. Any one give some advice. Thanks, Jin Hee -- 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
[gmx-users] Freeze backbone & Pressure scaling more than 1%
Dear all When I run produnction run using freeze backbone in GROMACS 4.0.5, the error was shown. But I didn't use freeze backboone, the error wasn't shown. Step 1 Warning: Pressure scaling more than 1%. I changed "tau_p" value from 0.5 to 5 in md.mdp file, but the above error was shown. I don't know how to solve it. Any one give some advice. Thanks, Jin Hee -- 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
Re: [gmx-users] do_dssp Installation instructions in case you have errors
Kirill Bessonov wrote: I had seen people having trouble with do_dssp and that Error line 471 error. Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro /dev/null 2> /dev/null So I would like to spill some light on the issue and make documentation better to understand after hours fiddling with source code. Why did you spend hours looking at the source code? The documentation in do_dssp -h clearly specifies the need to set the executable name in the environment variable DSSP. The documentation and the error message upon non-existence of the path to DSSP could be improved such that it is not specific to C-shell. If you have this error this means that dssp executable was not found even though the PATH was set correctly (i.e. DSSP path variable) It's not a path variable - you've made a wrong assumption. If you look at the source code the fexist funciton checks if there is any file in directory and returns true, so if you have any file there the code will run through and fail on line: sprintf(dssp,"%s %s %s %s > /dev/null %s", dptr,bDoAccSurf?"":"-na",pdbfile,tmpfile,bVerbose?"":"2> /dev/null"); where dssp is the buffer of charcters and dptr is the pointer to the dssp executable file (not the folder!) And that is the main source of errors, improper definition of directory pointer to the executable. That's not the mistake. The "mistake" is GROMACS only checking for existence of the contents of DSSP and assuming the user has read the documentation. If the user erroneously specifies a path which exists, the check succeeds. It could/should check for existence, being executable, not being a directory, being non-zero size, not being a Unix virus, not being an alias for "sudo rm -rf /", etc. but one can't protect the user from everything :-) Mark Solution: To correct this mistake add to the path the name of the dssp exectutable. E.g. if you named it dssp and put it in your home folder. Add to .bash_profile DSSP=/home/dssp (where dssp is not a FOLDER but name of executable) If you named executable dsspmbi DSSP=/home/dsspmbi (and again dsspmbi is the name of executable) This will define the location of dssp executable properly and you would not see any weird complicated errors coming up. Hope it helps -- 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
Re: [gmx-users] Check for bad contacts and/or reduce the timestep
nishap.pa...@utoronto.ca wrote: Steepest Descents converged to machine precision in 34 steps, but did not reach the requested Fmax < 10. Potential Energy = -3.7206969e+04 Maximum force = 2.0111207e+04 on atom 1217 Norm of force = 6.9283209e+02 I don't understand constraints I need to turn off, since I haven't mentioned any in my grompp file. This is just generic advice that mdrun provides. The fact is your starting structure contains atomic overlap or clashes that cannot be resolved by energy minimization. Have a look at the trajectory and see if you can get some insight into where things are going wrong (since problematic atom numbers are being printed, and perhaps re-consider how you built your system. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
Re: [gmx-users] Check for bad contacts and/or reduce the timestep
- Forwarded message from nishap.pa...@utoronto.ca - Date: Mon, 14 Dec 2009 14:06:30 -0500 From: nishap.pa...@utoronto.ca Reply-To: nishap.pa...@utoronto.ca Subject: Re: [gmx-users] Check for bad contacts and/or reduce the timestep To: "Justin A. Lemkul" I tried to run minimization step and I got the following error: Steepest Descents: Tolerance (Fmax) = 1.0e+01 Number of steps=25000 Step=1, Dmax= 1.0e-02 nm, Epot= 1.57470e+09 Fmax= 2.12566e+11, atom= 4973 Step=2, Dmax= 1.2e-02 nm, Epot= 2.42785e+08 Fmax= 2.02821e+10, atom= 4985 Step=3, Dmax= 1.4e-02 nm, Epot= 6.83525e+07 Fmax= 2.24629e+09, atom= 4973 Step=4, Dmax= 1.7e-02 nm, Epot= 1.36192e+07 Fmax= 2.34481e+08, atom= 4985 Step=5, Dmax= 2.1e-02 nm, Epot= 3.37948e+06 Fmax= 2.50839e+07, atom= 4973 Step=6, Dmax= 2.5e-02 nm, Epot= 9.58580e+05 Fmax= 2.79175e+06, atom= 1321 Step=7, Dmax= 3.0e-02 nm, Epot= 2.98861e+05 Fmax= 3.83032e+06, atom= 4973 Step=8, Dmax= 3.6e-02 nm, Epot= 2.15478e+05 Fmax= 5.79850e+05, atom= 4973 Step=9, Dmax= 4.3e-02 nm, Epot= 7.16581e+04 Fmax= 1.12895e+06, atom= 4973 Step= 10, Dmax= 5.2e-02 nm, Epot= 4.39860e+04 Fmax= 7.57820e+04, atom= 101 t = 0.022 ps: Water molecule starting at atom 101 can not be settled. Check for bad contacts and/or reduce the timestep. Back Off! I just backed up step11b.pdb to ./#step11b.pdb.6# Back Off! I just backed up step11c.pdb to ./#step11c.pdb.6# Wrote pdb files with previous and current coordinates Step= 11, Dmax= 6.2e-02 nm, Epot= -1.94430e+04 Fmax= 7.60249e+04, atom= 102 Step= 12, Dmax= 7.4e-02 nm, Epot= -2.29926e+04 Fmax= 3.21409e+05, atom= 4917 t = 0.026 ps: Water molecule starting at atom 4917 can not be settled. Check for bad contacts and/or reduce the timestep. Back Off! I just backed up step13b.pdb to ./#step13b.pdb.6# Back Off! I just backed up step13c.pdb to ./#step13c.pdb.6# Wrote pdb files with previous and current coordinates Step= 14, Dmax= 4.5e-02 nm, Epot= -2.80812e+04 Fmax= 1.42056e+04, atom= 9577 Step= 15, Dmax= 5.3e-02 nm, Epot= -3.28009e+04 Fmax= 1.37135e+05, atom= 4893 t = 0.032 ps: Water molecule starting at atom 4893 can not be settled. Check for bad contacts and/or reduce the timestep. Back Off! I just backed up step16b.pdb to ./#step16b.pdb.6# Back Off! I just backed up step16c.pdb to ./#step16c.pdb.6# Wrote pdb files with previous and current coordinates Step= 16, Dmax= 6.4e-02 nm, Epot= -3.72070e+04 Fmax= 2.01112e+04, atom= 1217 t = 0.034 ps: Water molecule starting at atom 4917 can not be settled. Check for bad contacts and/or reduce the timestep. Back Off! I just backed up step17b.pdb to ./#step17b.pdb.2# Back Off! I just backed up step17c.pdb to ./#step17c.pdb.2# Wrote pdb files with previous and current coordinates Step= 33, Dmax= 1.2e-06 nm, Epot= -1.10597e+04 Fmax= 1.29469e+06, atom= 4893 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 34 steps, but did not reach the requested Fmax < 10. Potential Energy = -3.7206969e+04 Maximum force = 2.0111207e+04 on atom 1217 Norm of force = 6.9283209e+02 I don't understand constraints I need to turn off, since I haven't mentioned any in my grompp file. -Nisha nishap.pa...@utoronto.ca wrote: Hi, I am trying to run a simulation with 1360 Tip4p water molecules and one methane molecule (Box size: 35.500 35.3371 35.500 and Total 5541 atoms) but I am getting the error: t = 0.000 ps: Water molecule starting at atom 5433 can not be settled. Check for bad contacts and/or reduce the timestep. Have you done sufficient energy minimization? General information can be found within the wiki pages of the Gromacs site, i.e.: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings -Justin Here is my grompp. file : ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 0.0 dt = 0.002 nsteps = 25000 ; number of steps for center of mass motion removal = nstcomm = 1 ENERGY MINIMIZATION OPTIONS emtol= 1 emstep = 0.01 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 1000 nstvout = 1000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 0 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 100 xtc_precision= 1000 ; This selects the subset of atoms for the xtc file
Re: [gmx-users] Check for bad contacts and/or reduce the timestep
nishap.pa...@utoronto.ca wrote: Hi, I am trying to run a simulation with 1360 Tip4p water molecules and one methane molecule (Box size: 35.500 35.3371 35.500 and Total 5541 atoms) but I am getting the error: t = 0.000 ps: Water molecule starting at atom 5433 can not be settled. Check for bad contacts and/or reduce the timestep. Have you done sufficient energy minimization? General information can be found within the wiki pages of the Gromacs site, i.e.: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings -Justin Here is my grompp. file : ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 0.0 dt = 0.002 nsteps = 25000 ; number of steps for center of mass motion removal = nstcomm = 1 ENERGY MINIMIZATION OPTIONS emtol= 1 emstep = 0.01 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 1000 nstvout = 1000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 0 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 100 xtc_precision= 1000 ; This selects the subset of atoms for the xtc file. = ; Only the first group gets written out, it does not make sense = ; to have multiple groups. By default all atoms will be written = xtc_grps = ; Selection of energy groups = energygrps = CH4 SOL ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 1.0 ; ns algorithm (simple or grid) = ns_type = grid ; nblist cut-off = rlist= 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulomb_type = pme rcoulomb_switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r= 1.0 epsilon_rf = 0 ; Method for doing Van der Waals = vdw_type = Cut-off ; cut-off lengths= rvdw_switch = 0 rvdw = 1.0 dispcorr = enerpres ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = v-rescale ; Groups to couple separately = tc-grps = system ; Time constant (ps) and reference temperature (K) = tau_t= 0.1 ref_t= 300 ; Pressure coupling = Pcoupl = Berendsen ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 1.0 compressibility = 4.6e-5 ref_p= 1 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 300 gen_seed = 171533 I am new to this, so any inputs would be appreciated. Thanks Nisha -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
[gmx-users] Check for bad contacts and/or reduce the timestep
Hi, I am trying to run a simulation with 1360 Tip4p water molecules and one methane molecule (Box size: 35.500 35.3371 35.500 and Total 5541 atoms) but I am getting the error: t = 0.000 ps: Water molecule starting at atom 5433 can not be settled. Check for bad contacts and/or reduce the timestep. Here is my grompp. file : ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 0.0 dt = 0.002 nsteps = 25000 ; number of steps for center of mass motion removal = nstcomm = 1 ENERGY MINIMIZATION OPTIONS emtol= 1 emstep = 0.01 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 1000 nstvout = 1000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 0 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 100 xtc_precision= 1000 ; This selects the subset of atoms for the xtc file. = ; Only the first group gets written out, it does not make sense = ; to have multiple groups. By default all atoms will be written = xtc_grps = ; Selection of energy groups = energygrps = CH4 SOL ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 1.0 ; ns algorithm (simple or grid) = ns_type = grid ; nblist cut-off = rlist= 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulomb_type = pme rcoulomb_switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r= 1.0 epsilon_rf = 0 ; Method for doing Van der Waals = vdw_type = Cut-off ; cut-off lengths= rvdw_switch = 0 rvdw = 1.0 dispcorr = enerpres ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = v-rescale ; Groups to couple separately = tc-grps = system ; Time constant (ps) and reference temperature (K) = tau_t= 0.1 ref_t= 300 ; Pressure coupling = Pcoupl = Berendsen ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 1.0 compressibility = 4.6e-5 ref_p= 1 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 300 gen_seed = 171533 I am new to this, so any inputs would be appreciated. Thanks Nisha -- 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
Re: [gmx-users] Can I combine my old and new .trr files?
On Dec 14, 2009, at 6:08 PM, Nilesh Dhumal wrote: Hey All, I am running simulation for 20 ns. My simulation got crashed after 171 steps. I continiued the simulation with following command. tpbconv -s 3.tpr -o 3n.tpr this step is not needed you can use the same tpr in your following command. /opt/mpich_intel/ch-p4/bin/mpirun -machinefile cp -np 2 /usr/local/gromacs/bin/mdrun_mpi -s 3n.tpr -cpi state_prev.cpt -append The prog. is writing all new data to traj.part0002.trr, md.part0002.log, ener.part0002.edr (old files: 3.trr, 3.log and 3.edr) After simulation gets over then Can I combine my old and new files? yes use trjcat for this. Thanks Nilesh -- 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 -- 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
[gmx-users] Can I combine my old and new .trr files?
Hey All, I am running simulation for 20 ns. My simulation got crashed after 171 steps. I continiued the simulation with following command. tpbconv -s 3.tpr -o 3n.tpr /opt/mpich_intel/ch-p4/bin/mpirun -machinefile cp -np 2 /usr/local/gromacs/bin/mdrun_mpi -s 3n.tpr -cpi state_prev.cpt -append The prog. is writing all new data to traj.part0002.trr, md.part0002.log, ener.part0002.edr (old files: 3.trr, 3.log and 3.edr) After simulation gets over then Can I combine my old and new files? Thanks Nilesh -- 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
[gmx-users] do_dssp Installation instructions in case you have errors
I had seen people having trouble with do_dssp and that Error line 471 error. Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro /dev/null 2> /dev/null So I would like to spill some light on the issue and make documentation better to understand after hours fiddling with source code. If you have this error this means that dssp executable was not found even though the PATH was set correctly (i.e. DSSP path variable) If you look at the source code the fexist funciton checks if there is any file in directory and returns true, so if you have any file there the code will run through and fail on line: sprintf(dssp,"%s %s %s %s > /dev/null %s", dptr,bDoAccSurf?"":"-na",pdbfile,tmpfile,bVerbose?"":"2> /dev/null"); where dssp is the buffer of charcters and dptr is the pointer to the dssp executable file (not the folder!) And that is the main source of errors, improper definition of directory pointer to the executable. Solution: To correct this mistake add to the path the name of the dssp exectutable. E.g. if you named it dssp and put it in your home folder. Add to .bash_profile DSSP=/home/dssp (where dssp is not a FOLDER but name of executable) If you named executable dsspmbi DSSP=/home/dsspmbi (and again dsspmbi is the name of executable) This will define the location of dssp executable properly and you would not see any weird complicated errors coming up. Hope it helps -- 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
Re: [gmx-users] free energy perturbation
I will try the second solution you proposed (which seems more flexible). So, I should edit the top file (as explained in the "Topologies/File formats/Topologies for free energy calculations" section of the manual). And I should NOT use "couple-moltype" anymore, which is just a shortcut for the standard case of switching a single molecule. Right? Thanks a lot Berk. Giovanni On Mon, Dec 14, 2009 at 3:49 PM, Berk Hess wrote: > > >> From: giovanni.bu...@gmail.com >> Date: Mon, 14 Dec 2009 13:47:37 +0100 >> To: gmx-users@gromacs.org >> Subject: [gmx-users] free energy perturbation >> >> Dear all, >> >> I am using GROMACS with free-energy perturbation to switch off a >> molecule gradually. If I understand correctly, the parameter >> "couple-moltype" is used to select which molecule to switch off. Is it >> possible to switch off *two* molecules at the same time? (e.g. a >> charged molecule and a neutralizing ion). > > I have not implemented this yet. > It would indeed be useful. > >> >> In case not, is there any problem related to the fact that in one of >> the topologies the total charge is not zero? > > Yes, this will create problems, because you are then also calculating the > cost > of building up a uniform backbground charge, both in case of PME and RF. > > Note that free-energies of solvation of ions are huge numbers and are > relatively > difficult to determine, both in simulation and in experiment. > > There are two way to work around this problem: > Put both molecules together in one moleculetype definition. > Or simply manually set the LJ and charge of the ion to zero in the A or B > state topology. > > Berk > >> >> Thanks a lot, >> >> Giovanni >> -- >> gmx-users mailing list gmx-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 > > > New Windows 7: Simplify what you do everyday. Find the right PC for you. > -- > gmx-users mailing list gmx-us...@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 > -- 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
RE: [gmx-users] free energy perturbation
> From: giovanni.bu...@gmail.com > Date: Mon, 14 Dec 2009 13:47:37 +0100 > To: gmx-users@gromacs.org > Subject: [gmx-users] free energy perturbation > > Dear all, > > I am using GROMACS with free-energy perturbation to switch off a > molecule gradually. If I understand correctly, the parameter > "couple-moltype" is used to select which molecule to switch off. Is it > possible to switch off *two* molecules at the same time? (e.g. a > charged molecule and a neutralizing ion). I have not implemented this yet. It would indeed be useful. > > In case not, is there any problem related to the fact that in one of > the topologies the total charge is not zero? Yes, this will create problems, because you are then also calculating the cost of building up a uniform backbground charge, both in case of PME and RF. Note that free-energies of solvation of ions are huge numbers and are relatively difficult to determine, both in simulation and in experiment. There are two way to work around this problem: Put both molecules together in one moleculetype definition. Or simply manually set the LJ and charge of the ion to zero in the A or B state topology. Berk > > Thanks a lot, > > Giovanni > -- > 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 _ New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop-- 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
[gmx-users] free energy perturbation
Dear all, I am using GROMACS with free-energy perturbation to switch off a molecule gradually. If I understand correctly, the parameter "couple-moltype" is used to select which molecule to switch off. Is it possible to switch off *two* molecules at the same time? (e.g. a charged molecule and a neutralizing ion). In case not, is there any problem related to the fact that in one of the topologies the total charge is not zero? Thanks a lot, Giovanni -- 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
Re: [gmx-users] superimposition
leila karami wrote: dear Mark is there another way to obtain superimposed structure of initial and final structures. please guide me Load two structures into VMD separately. Alternatively, tell us exactly what you've tried and we might see why it didn't work. Without knowing your command lines, all anybody can say is "you did it wrong". Mark -- 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
Re: [gmx-users] superimposition
leila karami wrote: dear Mark is there another way to obtain superimposed structure of initial and final structures. please guide me g_confrms -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- 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
[gmx-users] superimposition
dear Mark is there another way to obtain superimposed structure of initial and final structures. please guide me -- 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
Re: [gmx-users] superimposition
leila karami wrote: Hi I used commands trjconv and trjcat for fitting and obtaining of superimposed structure between initial and final structure but when I open pdb file containing superimposed structure with VMD, 2 structure were shown but there is some exessive bonds. I'm not sure about your use of "superimposed" here. http://www.gromacs.org/Documentation/Terminology/Average_Structure or http://www.gromacs.org/About_Gromacs/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds probably answer your issue. If you've somehow edited your file or forced VMD to read the two structures as one, then of course there will be excess bonds. Mark -- 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
[gmx-users] superimposition
Hi I used commands trjconv and trjcat for fitting and obtaining of superimposed structure between initial and final structure but when I open pdb file containing superimposed structure with VMD, 2 structure were shown but there is some exessive bonds. please guide me. -- 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
