Re: [gmx-users] gmx conver-tpr error
Dear Dr. Justin, Thank you very much for the reply. I'm sure, I used -extend for the gmx convert-tpr. How can I solve this problem? Appreciate, if you could help me. Thank you. On Wed, May 30, 2018 at 9:51 PM, Justin Lemkul wrote: > > > On 5/30/18 5:51 AM, Amali Guruge wrote: > >> Dear Gromacs users, >> >> I did a simulation for a 50 ns and I want to extend it by anther 50 ns. >> Therefore, I used the command, >> gmx convert-tpr -s run01.tpr -extend 5 -o run02.tpr >> But I got the error, 'You've simulated long enough. Not writing tpr file.' >> >> How can I solve the problem? >> > > Are you sure that was your exact command? You didn't accidentally type > "-until" rather than "-extend" in your command? Any use of -extend > shouldn't trigger that error, but -until would do exactly that in this > instance. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx conver-tpr error
Dear Gromacs users, I did a simulation for a 50 ns and I want to extend it by anther 50 ns. Therefore, I used the command, gmx convert-tpr -s run01.tpr -extend 5 -o run02.tpr But I got the error, 'You've simulated long enough. Not writing tpr file.' How can I solve the problem? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Solvation of the bilayer
Dear Gromacs users, I have a bilayer in xy plane. I tried to solvate the bilayer (sur_bilayer.pdb) with water molecules using gmx solvate. I used the command; gmx solvate -cp sur_bilayer.pdb -maxsol 28197 -o sur_water_bilayer.pdb However, water molecules are not distributed in the hydrophilic layers in the xy plane as I wanted. How can I solve this problem? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs simulation with PEG
Dear Gromacs Users, Thank you very much. On Mon, Nov 13, 2017 at 9:56 AM, Justin Lemkul wrote: > > > On 11/12/17 5:51 PM, Amali Guruge wrote: > >> Dear Gromacs users, >> >> I tried to simulate a system which contains PEG and water. According to >> the >> phase diagram of PEG, it should form micells after the simulation. >> However, >> after the simulation PEG doesn't form micells. What could be the reason >> for >> this. Can anyone help me. >> > > Any number of things, none of which you've described to us - insufficient > simulation time, inadequate force field, mismatching conditions (i.e. not > replicating experiment exactly), etc. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Gromacs simulation with PEG
Dear Gromacs users, I tried to simulate a system which contains PEG and water. According to the phase diagram of PEG, it should form micells after the simulation. However, after the simulation PEG doesn't form micells. What could be the reason for this. Can anyone help me. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Too many LINCS warnings when changed the time step
Dear Dr. Justin, Thank you very much for the reply. If I keep the 0.005 as the time step, what steps should be followed in-order to avoid the LINCS warnings? Appreciate if you can comment on this. Thank you. On Thu, Nov 9, 2017 at 12:46 PM, Justin Lemkul wrote: > > > On 11/8/17 8:45 PM, Amali Guruge wrote: > >> Dear Gromacs users, >> >> I did energy minimization step and started the equilibration run. However, >> when I changed the time step 0.002 to to 0.005, it gave an error; Too many >> LINCS warnings. What could be the reason for this? The simulation was >> worked without an error until I changed the time step. Appreciate if >> anyone >> can give me a solution. >> > > A 5-fs timestep is only stable is using some topological modification like > virtual sites and/or hydrogen mass repartitioning. Generally, a 2-fs > timestep is an upper limit without such tricks. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Too many LINCS warnings when changed the time step
Dear Gromacs users, I did energy minimization step and started the equilibration run. However, when I changed the time step 0.002 to to 0.005, it gave an error; Too many LINCS warnings. What could be the reason for this? The simulation was worked without an error until I changed the time step. Appreciate if anyone can give me a solution. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] tc-groups in mdp file
Dear gmx users, My system contains ~ 700 polyethylene glycol (PEG) molecules and ~96000 water molecules (SOL). I would like to know that, do I have to use two groups to control the temperature or just use one? Can anyone help me? Thank you. Sincerely, A. G. G -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Water molecule can not be settled
Dear Gromacs users, My system contains water molecules and polyethylene glycol molecules. I generated the box (15.2*15.2*15.2 nm*3) using genbox command. Thereafter, PEG molecules were added using gmx insert-molecules and solvated with gmx solvate. When I tried to run md, I got the following error. step 1802: Water molecule starting at atom 93528 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Segmentation fault (core dumped) my rum.mdp file contains following parameters. integrator= md dt= 0.005 nsteps= 100 comm_mode= linear ; nstxout= 50 nstlog= 1000 nstenergy= 50 nstxtcout= 1 ; cutoff-scheme = Verlet nstlist = 10 ns_type = grid pbc = xyz rlist = 1.4 ; coulombtype = PME rcoulomb= 1.4 epsilon_r = 1 rvdw= 1.4 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 DispCorr= EnerPres ; Tcoupl= v-rescale tc-grps= System tau_t= .1 ref_t= 298 ; Pcoupl= parrinello-rahman Pcoupltype= isotropic tau_p= 2.0 compressibility= 4.5e-5 ref_p= 1.0 ; gen_vel= no ; constraints= all-bonds constraint_algorithm= lincs lincs_order= 8 Can anyone help me to solve the error. The most of the people commented previously that this error is due to a bad starting structure. If it is the reason, how can I correct it. Thank you. Sincerely, A Guruge -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy Minimization Error
Dear Gromacs users, When I tried to run the equilibration run, it gave several LINCS WARNINGS. However, that equilibration run is completed by the Gromacs. Do I have to concern about these warnings or can I ignore those? Thank you. Sincerely, A. Guruge On Fri, Oct 20, 2017 at 11:22 AM, Justin Lemkul wrote: > > > On 10/19/17 8:21 PM, Amali Guruge wrote: > >> Dear Gromacs users, >> >> Thank you very much for the reply. My concern is "step 11: One or more >> water molecules can not be settled. >> Check for bad contacts and/or reduce the timestep if appropriate". What >> should I do to avoid it? >> > > That happens often during minimization, especially the early steps. If it > doesn't come back up again, it's fine. It should never happen during MD. > > -Justin > > > Thank you. >> >> On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul wrote: >> >> >>> On 10/19/17 8:10 PM, Amali Guruge wrote: >>> >>> Dear Gromacs Users, >>>> >>>> I tried to energy minimize my system using the steep integrator. >>>> However, >>>> it gave the following message. >>>> >>>> Steepest Descents: >>>> Tolerance (Fmax) = 5.0e+02 >>>> Number of steps= 2000 >>>> Step=0, Dmax= 1.0e-02 nm, Epot= 3.96157e+06 Fmax= 1.00697e+06, >>>> atom= >>>> 14611 >>>> Step=1, Dmax= 1.0e-02 nm, Epot= 2.99970e+06 Fmax= 4.04778e+05, >>>> atom= >>>> 18527 >>>> Step=2, Dmax= 1.2e-02 nm, Epot= 1.54766e+06 Fmax= 1.52387e+05, >>>> atom= >>>> 1005 >>>> Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, >>>> atom= >>>> 6994 >>>> Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, >>>> atom= >>>> 58902 >>>> Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, >>>> atom= >>>> 515 >>>> Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, >>>> atom= >>>> 188631 >>>> Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, >>>> atom= >>>> 188631 >>>> Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, >>>> atom= >>>> 188631 >>>> Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, >>>> atom= >>>> 188631 >>>> Step= 10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, >>>> atom= >>>> 188631 >>>> >>>> step 11: One or more water molecules can not be settled. >>>> Check for bad contacts and/or reduce the timestep if appropriate. >>>> >>>> After 2000 steps it says, >>>> >>>> Steepest Descents did not converge to Fmax < 500 in 2001 steps. >>>> Potential Energy = -4.6310655e+06 >>>> Maximum force = 6.7453154e+03 on atom 18769 >>>> Norm of force = 3.3632809e+01 >>>> >>>> Simulation ended prematurely, no performance report will be written. >>>> >>>> >>>> my em.mdp file contains following parameters. >>>> >>>> integrator= steep; simulation algorithm >>>> dt= 0.002; time step (ps) >>>> nsteps= 2000; # steps >>>> comm_mode= linear; c.o.m. motion reset >>>> ; >>>> ;Energy Minimization >>>> emtol= 500; converged F lt value (kJ mol-1 >>>> nm-1) >>>> emstep= 0.01 ; initial step size (nm) >>>> ; >>>> ;Output Control >>>> nstxout= 5 ; write coordinates to .trr >>>> nstvout= 5; write velocities to .trr >>>> nstlog= 5; write energies to .log >>>> nstenergy= 1; write energies to .edr >>>> ; >>>> ;Neightbour Searching >>>> cutoff-scheme = Verlet; scheme used for >>>> generating pair list >>>> nstlist = 10 ; update neighbour list >>>> ns_type= grid; neighbour list method >>>> pbc= xyz; periodic boundary conditions >>>> rlist= 0.9 ; cut-off for short-range neighb
Re: [gmx-users] Energy Minimization Error
Dear Gromacs users, Thank you very much for the reply. My concern is "step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate". What should I do to avoid it? Thank you. On Fri, Oct 20, 2017 at 11:12 AM, Justin Lemkul wrote: > > > On 10/19/17 8:10 PM, Amali Guruge wrote: > >> Dear Gromacs Users, >> >> I tried to energy minimize my system using the steep integrator. However, >> it gave the following message. >> >> Steepest Descents: >> Tolerance (Fmax) = 5.0e+02 >> Number of steps= 2000 >> Step=0, Dmax= 1.0e-02 nm, Epot= 3.96157e+06 Fmax= 1.00697e+06, atom= >> 14611 >> Step=1, Dmax= 1.0e-02 nm, Epot= 2.99970e+06 Fmax= 4.04778e+05, atom= >> 18527 >> Step=2, Dmax= 1.2e-02 nm, Epot= 1.54766e+06 Fmax= 1.52387e+05, atom= >> 1005 >> Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom= >> 6994 >> Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom= >> 58902 >> Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom= >> 515 >> Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom= >> 188631 >> Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom= >> 188631 >> Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom= >> 188631 >> Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom= >> 188631 >> Step= 10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom= >> 188631 >> >> step 11: One or more water molecules can not be settled. >> Check for bad contacts and/or reduce the timestep if appropriate. >> >> After 2000 steps it says, >> >> Steepest Descents did not converge to Fmax < 500 in 2001 steps. >> Potential Energy = -4.6310655e+06 >> Maximum force = 6.7453154e+03 on atom 18769 >> Norm of force = 3.3632809e+01 >> >> Simulation ended prematurely, no performance report will be written. >> >> >> my em.mdp file contains following parameters. >> >> integrator= steep; simulation algorithm >> dt= 0.002; time step (ps) >> nsteps= 2000; # steps >> comm_mode= linear; c.o.m. motion reset >> ; >> ;Energy Minimization >> emtol= 500; converged F lt value (kJ mol-1 nm-1) >> emstep= 0.01 ; initial step size (nm) >> ; >> ;Output Control >> nstxout= 5 ; write coordinates to .trr >> nstvout= 5; write velocities to .trr >> nstlog= 5; write energies to .log >> nstenergy= 1; write energies to .edr >> ; >> ;Neightbour Searching >> cutoff-scheme = Verlet; scheme used for >> generating pair list >> nstlist = 10 ; update neighbour list >> ns_type= grid; neighbour list method >> pbc= xyz; periodic boundary conditions >> rlist= 0.9 ; cut-off for short-range neighbour >> (nm) >> ; >> ;Electrostatics and VdW >> coulombtype= PME; type of coulomb interaction >> rcoulomb= 0.9; cut-off distance for coulomb >> epsilon_r= 1; dielectric constant >> rvdw= 0.9; cut-off for vdw >> fourierspacing= 0.12; maximum grid spacing for FFT >> pme_order= 4; interpolation order for PME >> ewald_rtol= 1e-5; relative strength of Ewald-shifted >> DispCorr= EnerPres ; long range dispersion >> corrections >> ; >> ;Temperature Coupling >> Tcoupl= no; type of temperature coupling >> ; >> ;Pressure Coupling >> Pcoupl= no ; type of pressure coupling >> ; >> ;Velocity Generation >> gen_vel= no ; generate initial velocities >> ; >> ;Bonds >> constraints= none; bond constraint type >> >> I used gmx solvate to add water molecules to the system. >> >> How could I get rid of bad contacts of water molecules? Appreciate if >> anyone help me to solve the problem. >> > > mdrun stopped after 2000 steps because you told it to. You need to > minimize fur
[gmx-users] Energy Minimization Error
Dear Gromacs Users, I tried to energy minimize my system using the steep integrator. However, it gave the following message. Steepest Descents: Tolerance (Fmax) = 5.0e+02 Number of steps= 2000 Step=0, Dmax= 1.0e-02 nm, Epot= 3.96157e+06 Fmax= 1.00697e+06, atom= 14611 Step=1, Dmax= 1.0e-02 nm, Epot= 2.99970e+06 Fmax= 4.04778e+05, atom= 18527 Step=2, Dmax= 1.2e-02 nm, Epot= 1.54766e+06 Fmax= 1.52387e+05, atom= 1005 Step=3, Dmax= 1.4e-02 nm, Epot= -6.18032e+04 Fmax= 6.75685e+04, atom= 6994 Step=4, Dmax= 1.7e-02 nm, Epot= -1.18915e+06 Fmax= 2.96211e+04, atom= 58902 Step=5, Dmax= 2.1e-02 nm, Epot= -1.97299e+06 Fmax= 1.31669e+04, atom= 515 Step=6, Dmax= 2.5e-02 nm, Epot= -2.53642e+06 Fmax= 1.74841e+04, atom= 188631 Step=7, Dmax= 3.0e-02 nm, Epot= -2.72242e+06 Fmax= 2.62746e+04, atom= 188631 Step=8, Dmax= 3.6e-02 nm, Epot= -2.81986e+06 Fmax= 2.75458e+04, atom= 188631 Step=9, Dmax= 4.3e-02 nm, Epot= -2.90598e+06 Fmax= 1.80180e+04, atom= 188631 Step= 10, Dmax= 5.2e-02 nm, Epot= -3.02588e+06 Fmax= 5.79279e+04, atom= 188631 step 11: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. After 2000 steps it says, Steepest Descents did not converge to Fmax < 500 in 2001 steps. Potential Energy = -4.6310655e+06 Maximum force = 6.7453154e+03 on atom 18769 Norm of force = 3.3632809e+01 Simulation ended prematurely, no performance report will be written. my em.mdp file contains following parameters. integrator= steep; simulation algorithm dt= 0.002; time step (ps) nsteps= 2000; # steps comm_mode= linear; c.o.m. motion reset ; ;Energy Minimization emtol= 500; converged F lt value (kJ mol-1 nm-1) emstep= 0.01 ; initial step size (nm) ; ;Output Control nstxout= 5 ; write coordinates to .trr nstvout= 5; write velocities to .trr nstlog= 5; write energies to .log nstenergy= 1; write energies to .edr ; ;Neightbour Searching cutoff-scheme = Verlet; scheme used for generating pair list nstlist = 10 ; update neighbour list ns_type= grid; neighbour list method pbc= xyz; periodic boundary conditions rlist= 0.9 ; cut-off for short-range neighbour (nm) ; ;Electrostatics and VdW coulombtype= PME; type of coulomb interaction rcoulomb= 0.9; cut-off distance for coulomb epsilon_r= 1; dielectric constant rvdw= 0.9; cut-off for vdw fourierspacing= 0.12; maximum grid spacing for FFT pme_order= 4; interpolation order for PME ewald_rtol= 1e-5; relative strength of Ewald-shifted DispCorr= EnerPres ; long range dispersion corrections ; ;Temperature Coupling Tcoupl= no; type of temperature coupling ; ;Pressure Coupling Pcoupl= no ; type of pressure coupling ; ;Velocity Generation gen_vel= no ; generate initial velocities ; ;Bonds constraints= none; bond constraint type I used gmx solvate to add water molecules to the system. How could I get rid of bad contacts of water molecules? Appreciate if anyone help me to solve the problem. Thank you. Sincerely, A Guruge -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] grompp error
Dear Gromacs users, I got the following error when I tried to run grompp. ERROR 1 [file system.top, line 18]: ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist I increased the box size and re-tried to run grompp,but it didn't work. The box size is 20*20*20 nm3. mdp file options are shown in below. Could you please anyone help me to solve this problem. Thank you. ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1.0; Stop minimization when the maximum force < 1.0 kJ/mol nsteps= 200; Maximum number of (minimization) steps to perform nstenergy= 10; Write energies to disk every nstenergy steps nstcalcenergy= 10; Calculate energy every step energygrps= System; Which energy group(s) to write to disk nstxout = 100 ; Frequency of writing to .trr file ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions cutoff-scheme = Verlet ns_type= simple; Method to determine neighbor list (simple, grid) coulombtype= cut-off; Treatment of long range electrostatic interactions rcoulomb= 1.0; long range electrostatic cut-off rvdw= 1.0; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= xyz; Periodic Boundary Conditions (yes/no) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fwd: Simulation of surfactant and water composition
-- Forwarded message -- From: Date: Thu, Oct 12, 2017 at 10:11 PM Subject: Simulation of surfactant and water composition To: amaligg2...@gmail.com You are not allowed to post to this mailing list, and your message has been automatically rejected. If you think that your messages are being rejected in error, contact the mailing list owner at gromacs.org_gmx-users-ow...@maillist.sys.kth.se. -- Forwarded message -- From: Amali Guruge To: gromacs.org_gmx-users@maillist.sys.kth.se Cc: Bcc: Date: Thu, 12 Oct 2017 22:11:11 +1100 Subject: Simulation of surfactant and water composition Dear Gromacs users, I want to model a system which contains surfactant molecules and water molecules. I also want to model the system with w/w 15% surfactant/water composition. Could you please guide me to model the system and do the simulation using Gromacs software. Appreciate, if anyone can give a tutorial to do the simulation in step by step. Thank you. Sincerely, A Guruge -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Hbond occupancy
Thank you very much Eric for the answer. Could you please give information regarding to the command use in this calculation? Thank you. On Fri, Jul 8, 2016 at 5:31 PM, Erik Marklund wrote: > gmx hbond > > > On 8 Jul 2016, at 12:24, Amali Guruge wrote: > > > > Dear All, > > > > Can anyone know how to calculate H bond occupancy with Gromacs? > > > > Thank you > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Hbond occupancy
Dear All, Can anyone know how to calculate H bond occupancy with Gromacs? Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Residue Numbers
Dear All, I used g_mmpbsa for free energy calculations. I competed contribution of residues to the binding energy using python script. Original residue number is available in final_contrib_energy.dat file. But we use energyMapIn.dat file for the graph plotting. In that file residue numbers are different, it always start with number one. How can I plot residue number vs energy contribution? Can anyone help me? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Values for pcon & ncon in G_mmpbsa
Dear All, In my MD simulation I only added counter ions (20 Na+ ions) to neutralize the system. Now I want to do MM_PBSA calculations for my MD runs. In order to do perform polar solvation energy, I have to define parameters pcon and ncon. According to my system what values should be assigned to those two parameters? If I assign 0 (zero) value for both parameters, is it correct? I don't have clear solution for this problem. Please can anyone help me? Thank you in advance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_mmpbsa python script error
Dear All, I installed g_mmpbsa tool for binding energy calculation for my GROMACS runs. When I gave the command, python MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a sasa.xvg I got the following error. python: can't open file 'MmPbSaStat.py': [Errno 2] No such file or directory Please can anyone help me to solve this problem. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Number of H bonds formed between ligand and amino acid residues
Thank you very much for the answer. How we identify residues involving in H bonds? In index file do we have to specify them? On Tue, Jun 28, 2016 at 11:45 AM, Subhomoi Borkotoky wrote: > Hello, > > Please use the "hbond" utility in gromacs. > > gmx hbond [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n > [<.ndx>]][-num [<.xvg>] > > > On Tue, Jun 28, 2016 at 11:24 AM, Amali Guruge > wrote: > > > Dear Gromacs users, > > > > I carried out 20 ns long MD simulation for my receptor-ligand complex > using > > Gromacs software. Now I want to calculate number of hydrogen bonds formed > > in the ligand and receptor corresponding to the residue number. Can > anyone > > help me? > > > > > > Thank you. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > Yours Sincerely, > -- > SUBHOMOI BORKOTOKY, > Centre for Bioinformatics > Pondicherry University > Pondicherry,INDIA. > > Alternate Email: subho...@mails.bicpu.edu.in > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Number of H bonds formed between ligand and amino acid residues
Dear Gromacs users, I carried out 20 ns long MD simulation for my receptor-ligand complex using Gromacs software. Now I want to calculate number of hydrogen bonds formed in the ligand and receptor corresponding to the residue number. Can anyone help me? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] MD Analysis
Dear Gromacs users, I completed 20 ns MD simulation using GROMACS software. Now I want to analyze the interactions were originally present and interactions were created/lost during the simulation. How can I do this? Can anyone help me? Can I use AMBERTool for this? Please anyone recommend me a tutorial regarding to this? Thank you in advance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Getting pdb structure
Thank you all... On Fri, Mar 25, 2016 at 7:52 PM, Erik Marklund wrote: > > > On 25 Mar 2016, at 14:06, Erik Marklund > wrote: > > > > gmx trjconv -f your.xc -s your.pr -o snapshot_at_8000.pdb -dump 8000 > > > > That should have been “-f your.xtc -s your.tpr”. I apologise on behalf of > autocorrect. > > >> On 25 Mar 2016, at 13:30, Amali Guruge wrote: > >> > >> Dear All, > >> > >> I want to get the pdb structure of the system in 8000 ps time. The whole > >> simulation contains 2 ps. How can I get the pdb structure of the > system > >> at that time? > >> Can anyone help me? > >> > >> Thank you. > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Getting pdb structure
Dear All, I want to get the pdb structure of the system in 8000 ps time. The whole simulation contains 2 ps. How can I get the pdb structure of the system at that time? Can anyone help me? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] SwissParam and Gromacs
Dear All, I submitted docked conformation of topotecan molecule to the SwissParam server and I got itp file. Then I did a molecular dynamic simulation using that itp file (I used Gromacs software with CHARMM27 force field) When I tried to run the command, grompp -c b4em.pdb -f em01.mdp -n index.ndx -p system.top -o em01.tpr it gave the following error. *Fatal error:Atomtype CB not found* I attached the itp file received from the server. Please help me to correct this error. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Amber03 parameters for PTR
Dear Prof. Justin, Thank you for the reply. Yes, I can use the parameters defined in that site, but I have to define the aminoacids.hbd file as well for PTR. How can I get that part? Thank you. On Wed, Oct 14, 2015 at 3:16 PM, Justin Lemkul wrote: > > > On 10/14/15 5:02 AM, Amali Guruge wrote: > >> Dear All, >> >> I want to do a molecular dynamic simulation for pdb ID 1K4T crystal >> structure using Amber03 force field. The structure contains >> phosphotyrosine >> (PTR). But parameters for PTR is not available in aminoacids.rtp file. >> Therefore can anyone help me to solve my problem. >> >> > http://sites.pharmacy.manchester.ac.uk/bryce/amber > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Amber03 parameters for PTR
Dear All, I want to do a molecular dynamic simulation for pdb ID 1K4T crystal structure using Amber03 force field. The structure contains phosphotyrosine (PTR). But parameters for PTR is not available in aminoacids.rtp file. Therefore can anyone help me to solve my problem. Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Atom OXT in PHE
Dear all, When I give pdb2gmx command I got the following error. Atom OXT in residue PHE 765 was not found in rtp entry PHE with 20 atoms while sorting. How can I fix this problem? Can anyone help me? Thank you... -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PTR is not found in residue topology database
Dear all, My enzyme contains PTR (phosphotyrosine) molecule which connect to the DNA. When I run the command pdb2gmx, it gives an error stating that PTR is not found in residue topology database. How can I fix this problem? Can anyone help me? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] MD with DNA double strand
Dear Gromacs users, I want to do a molecular dynamic simulation for my enzyme-ligand complex. The enzyme is topoisomerase I. I used the pdb id 1K4T for the simulation and I need to keep the DNA double strand with the enzyme. I replaced the 5'-sulfhydryl group into a 5'-hydroxyl group before starting the simulation. I gave the command 'pdb2gmx -f receptor.pdb -inter -p system.top -o recep01.pdb -ignh'. I selected AMBER99 as the force field while SPC/E was used as the water model. Then I got the following error. Fatal error: Atom O in residue DG 11 was not found in rtp entry DG with 33 atoms while sorting atoms. How can I solve this problem? Can anyone help me? Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.