Re: [gmx-users] Neutralizing
Thank you Parham You mean that it is not necessary to do QM/MM simulation? On Tuesday, March 8, 2016 11:13 AM, Parham Jabbarzadeh (Department of Biomedical Science) wrote: Dear Sir Use this command: gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral In this case, you don't need the number of ions. Kind Regards Parham J. K. ===== PhD candidate - Lecturer in drug discovery Faculty of Medicine and Health SciencesUniversity Putra MalaysiaMalaysia =====Publication ::: Featured Publication ::: Website ::: FaceBook On Tue, Mar 8, 2016 at 3:32 PM, mohammad r wrote: Hi everybody, I’ve generated a water-peptide system, now I want to neutralize it. Is adding adequate number of ions sufficient for neutralizing process or I should do QM/MM simulation for the this process? Thank you, Mohammad. -- 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] Embedding a protein into a lipid box using CGMD
Dear all during a part of martini tutorial it says: If a stable DPPC membrane with the wanted box dimensions is already available,�genbox�will be able to insert the peptides in the bilayer (the peptides have to be pre-centered and positioned to ensure their presence inside the membrane). so my question is that, now I have a solvated box ( 128 dppc with 2000 CG water ) and a pretein which is precentered as .gro file of solvated box. how can I embed them using genbox? I tried to do that but I failed. Any comment would be helpful and I really appreciate it. best regards Ali == Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir) Department of Mechanical Engineering Sharif University of Technology, Tehran, Iran -- 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 of only water - obtaining different pressure in the x , y and z directions
Hi, I am running a simulation which contains only water (using the spc216.gro coordinates and TIP3P model) in an NPT ensemble. I get different values for the average pressure in the x y and z directions. I am running the simulation for up to 10s in a 4nm side cube unit cell. I am using a Nose Hoover thermostat and a Parrinello-Rahman barostat applied isotropically, with target pressure 1 bar. The averages after 1ns are: Energy Average Err.Est. RMSD Tot-Drift --- Temperature 299.9990.000986.07906 0.00504098 (K) Pressure 1.3174 0.066350.061 -0.14372 (bar) Box-X4.03960.00013 0.00874048 -5.7234e-06 (nm) Box-Y4.03960.00013 0.00874048 -5.7234e-06 (nm) Box-Z4.03960.00013 0.00874048 -5.7234e-06 (nm) Pres-XX 1.11668 2 485.28 0.288761 (bar) Pres-YY -0.762405 1427.866-6.2632 (bar) Pres-ZZ 3.597922.4410.5465.54328 (bar) The averages over the 10 ns are : Energy Average Err.Est. RMSD Tot-Drift --- Temperature 300 8e-054.00951 0.000535848 (K) Pressure1.22566 0.0067275.993 -0.0289005 (bar) Box-X 4.039295.1e-05 0.00823878 0.000126042 (nm) Box-Y 4.039295.1e-05 0.00823878 0.000126042 (nm) Box-Z 4.039295.1e-05 0.00823878 0.000126042 (nm) Pres-XX 1.29387 0.73385.989 0.0898956 (bar) Pres-YY 1.35691 0.74378.8413.13618 (bar) Pres-ZZ 1.02621 0.84377.022 -3.31278 (bar) Why is the average pressure in the in each direction different? And why is the drift of the XX direction so much lower than in the YY and ZZ directions? Many thanks! -- 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] Extend to Embedding a protein into a lipid box using CGMD
Dear all based on my last question, consider My simulation box file is md.gro and my protein is CG.gro. now if you can, please write the desired command for me to embed this two file and have a lipid bilayer membrane embedded with protein please. best regards Ali == Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir) Department of Mechanical Engineering Sharif University of Technology, Tehran, Iran -- 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] Pressure of an energy minimized system
Dear all, I have a question regarding computation of pressure of an energy minimized (using steepest decent) system. I would expect that the pressure of an energy minimized system should have contribution only from the virial part of the pressure expression (as there is no temperature). However, when I am computing pressure using g_energy, the pressure (P_tot) and pressure computed from virial (P_vir = (-1/3Vol)*(Vir_xx+Vir_yy+Vir_z)/3)) are significantly different and P_tot is exactly six times P_vir. I am not able to understand the origin of this discrepancy. I would highly appreciate comments/suggestions from this forum. I would also very much appreciate any alternate suggestion for computing pressure of energy minimized structures. Thanks very much! Best, Rakesh Rakesh S. Singh, Ph.D. Postdoctoral Research Associate, Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544 -- 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] md of only water - obtaining different pressure in the x , y and z directions
Hi, pressure is an intrinsically macroscopic property (both in size and time), which we may compute for such small systems during such short simulations, but it does not behave ideally under these conditions. Remember that P and V are thermodynamically coupled variables and that liquid compressibility is low, so small volume fluctuations arising from pressure coupling to an external bath will produce wild instantaneous pressure fluctuations. If pressure matters for you for some reason, systems need to be much larger and time needs to be much longer. How larger and longer should they be? Take a look at your pressure fluctuations in a pressure-time plot or its histogram and notice that it spreads over hundreds or thousands of bars, so statistically meaningful averages can only be obtained if you manage to decrease that fluctuations, but fluctuations decrease as 1/SQRT(N), so increasing your system by a factor of 100 should decrease your pressure fluctuation by a factor of 10. It is hard to afford such large systems, so most people usually do pressure block averaging over long enough simulations. I hope it helps Andre On Tue, Mar 8, 2016 at 7:19 AM, Diez Fernandez, Amanda < amanda.die...@imperial.ac.uk> wrote: > Hi, > > I am running a simulation which contains only water (using the spc216.gro > coordinates and TIP3P model) in an NPT ensemble. > I get different values for the average pressure in the x y and z > directions. > I am running the simulation for up to 10s in a 4nm side cube unit cell. > I am using a Nose Hoover thermostat and a Parrinello-Rahman barostat > applied isotropically, with target pressure 1 bar. > > The averages after 1ns are: > > > Energy Average Err.Est. RMSD Tot-Drift > > > --- > > Temperature 299.9990.000986.07906 0.00504098 (K) > > Pressure 1.3174 0.066350.061 -0.14372 (bar) > > Box-X4.03960.00013 0.00874048 -5.7234e-06 (nm) > > Box-Y4.03960.00013 0.00874048 -5.7234e-06 (nm) > > Box-Z4.03960.00013 0.00874048 -5.7234e-06 (nm) > > Pres-XX 1.11668 2 485.28 0.288761 (bar) > > Pres-YY -0.762405 1427.866-6.2632 (bar) > > Pres-ZZ 3.597922.4410.5465.54328 (bar) > > > The averages over the 10 ns are : > > > Energy Average Err.Est. RMSD Tot-Drift > > > --- > > Temperature 300 8e-054.00951 0.000535848 (K) > > Pressure1.22566 0.0067275.993 -0.0289005 (bar) > > Box-X 4.039295.1e-05 0.00823878 0.000126042 (nm) > > Box-Y 4.039295.1e-05 0.00823878 0.000126042 (nm) > > Box-Z 4.039295.1e-05 0.00823878 0.000126042 (nm) > > Pres-XX 1.29387 0.73385.989 0.0898956 (bar) > > Pres-YY 1.35691 0.74378.8413.13618 (bar) > > Pres-ZZ 1.02621 0.84377.022 -3.31278 (bar) > > > > Why is the average pressure in the in each direction different? > > And why is the drift of the XX direction so much lower than in the YY and > ZZ directions? > > > Many thanks! > > -- > 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. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] Pressure of an energy minimized system
Hi, We discussed this recently at https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2015-October/008710.html. Whether it correctly computes the well defined quantity isn't known; neither does anybody know of a good use for it! Mark On Tue, 8 Mar 2016 14:31 Rakesh Sharan wrote: > Dear all, > > I have a question regarding computation of pressure of an energy minimized > (using steepest decent) system. I would expect that the pressure of an > energy minimized system should have contribution only from the virial part > of the pressure expression (as there is no temperature). However, when I am > computing pressure using g_energy, the pressure (P_tot) and pressure > computed from virial (P_vir = (-1/3Vol)*(Vir_xx+Vir_yy+Vir_z)/3)) are > significantly different and P_tot is exactly six times P_vir. I am not able > to understand the origin of this discrepancy. I would highly appreciate > comments/suggestions from this forum. I would also very much appreciate any > alternate suggestion for computing pressure of energy minimized structures. > > Thanks very much! > > Best, > Rakesh > > > Rakesh S. Singh, Ph.D. > Postdoctoral Research Associate, > Department of Chemical & Biological Engineering, > Princeton University, > Princeton, NJ 08544 > -- > 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.
Re: [gmx-users] Pressure of an energy minimized system
Thanks very much Mark! A good use of this quantity (pressure of energy minimized structures) is to understand the thermodynamic behavior of "inherent structures" (energy minimized structures). These inherent structures provide valuable information about the underlying potential energy landscape of a system and are becoming increasing popular in both biological (e. g. see http://www.pnas.org/content/103/14/5279.full ) and materials (e.g. see http://www.nature.com/nature/journal/v393/n6685/full/393554a0.html) sciences. I would highly recommend to keep this feature and make sure that it correctly computes the virial pressure. Best, Rakesh Rakesh S. Singh, Ph.D. Postdoctoral Research Associate, Department of Chemical & Biological Engineering, Princeton University, Princeton, NJ 08544 On Tue, Mar 8, 2016 at 9:41 AM, Mark Abraham wrote: > Hi, > > We discussed this recently at > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2015-October/008710.html > . > Whether it correctly computes the well defined quantity isn't known; > neither does anybody know of a good use for it! > > Mark > > On Tue, 8 Mar 2016 14:31 Rakesh Sharan wrote: > > > Dear all, > > > > I have a question regarding computation of pressure of an energy > minimized > > (using steepest decent) system. I would expect that the pressure of an > > energy minimized system should have contribution only from the virial > part > > of the pressure expression (as there is no temperature). However, when I > am > > computing pressure using g_energy, the pressure (P_tot) and pressure > > computed from virial (P_vir = (-1/3Vol)*(Vir_xx+Vir_yy+Vir_z)/3)) are > > significantly different and P_tot is exactly six times P_vir. I am not > able > > to understand the origin of this discrepancy. I would highly appreciate > > comments/suggestions from this forum. I would also very much appreciate > any > > alternate suggestion for computing pressure of energy minimized > structures. > > > > Thanks very much! > > > > Best, > > Rakesh > > > > > > Rakesh S. Singh, Ph.D. > > Postdoctoral Research Associate, > > Department of Chemical & Biological Engineering, > > Princeton University, > > Princeton, NJ 08544 > > -- > > 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.
Re: [gmx-users] unit cell vector warning
Hi, An update on the unit cell problem: when I make small changes in the angle, say change 89.45 to 89.00, the error disappears. I’m still getting the same warning. This is with version 5.1.2. Could this be a numerical precision issue (c_y is 0.05, see below) or a bug? I tried to run this without the protein, by just putting water and a few ions in the box. Best, Irem > On Mar 3, 2016, at 4:15 PM, Irem Altan wrote: > > Hi, > > I am trying to simulate a protein in its triclinic unit cell. During the > energy minimization and MD simulation, GROMACS prints the following out at > every step: > > WARNING: Found more than 12 triclinic correction vectors, ignoring some. > There is probably something wrong with your box. > 0.0e+00, 0.0e+00} > 3.89470e-01, 2.50360e+00 3.41610e-01 Box[1]={ 3.41610e-01, > 5.49000e-03, 5.26833e+00} > 2.91510e+00 Box (3x3): > 2.91510e+00, , 0.0e+00} >Box[1]={ Box[0]={ 0.0e+00 2.50360e+00 > 5.49000e-03, > > I checked the .gro file to see the unit cell vectors are listed correctly. > > The protein has the following sides and angles: > > a = 25.04, b = 29.41, c = 52.79, α = 89.45, β = 86.29, γ = 82.39 > > and I calculate the unit vectors to be: > > a = [ 25.036, 0. , 0. ] > b = [ 3.8947483 , 29.15096972, 0.] > c = [ 3.41611372, 0.05486764, 52.6816] > > and the .gro file has the line: > > 2.50360 2.91510 5.26833 0.0 0.0 0.38947 0.0 > 0.34161 0.00549 > > which seems to be correct. > > I have also verified that the conditions 3.1-3.3 listed on page 12 on the > manual for 5.1 to be correct. > > What could be the problem? > > Best, > Irem > -- > 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] Inconsistent shifts
Dear gmx users, i am using gmx 5.0.5 and i have a question concerning the error "There were x inconsistent shifts. Check your topology". I read some older posts about this error and do know that it comes together with something beeing wrong in the handling of pbc. I want to mention at the beginning that i have set "periodic-molecules = yes" in the mdp-file. My initial system consists of polyisoprene chains that contain up to 200 Monomer units. The system size is roughly 10x10x20 nm^3. It can be simulated (NPT) without any issues in parallel on 48 cores. Between the polymerchains i want to add sulfur bridges containing 2 sulfur atoms each. I am also able to stable run this system but when I use g_traj i get the above mentioned warning/error. I have also used the debug tool for g_traj to get more information. It said: "Guessed pbc = xyz from the box matrix mk_grey: shifts for atom 93303 due to atom 93302 are (1,2,0), should be (2,1,0) dx = (-0.177,0.106,0.0096)" From the source code i tried to understand how these shifts are calculated. But so far i did not suceed. Is there maybe someone who can explain it in detail? I hope i could clearly explain my problem. If thats not the case and more information is needed please contact me. Thanks in advance Jan -- 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] unit cell vector warning
Hi, How are you actually generating the coordinate file, and/or the box vectors? As far as I know, nobody's written down the set of vectors that should work sensibly, but it's likely that the gmx tools will write boxes that will definitely work later on... Mark On Tue, Mar 8, 2016 at 4:27 PM Irem Altan wrote: > Hi, > > An update on the unit cell problem: when I make small changes in the > angle, say change 89.45 to 89.00, the error disappears. I’m still getting > the same warning. This is with version 5.1.2. Could this be a numerical > precision issue (c_y is 0.05, see below) or a bug? I tried to run this > without the protein, by just putting water and a few ions in the box. > > Best, > Irem > > > On Mar 3, 2016, at 4:15 PM, Irem Altan wrote: > > > > Hi, > > > > I am trying to simulate a protein in its triclinic unit cell. During the > energy minimization and MD simulation, GROMACS prints the following out at > every step: > > > > WARNING: Found more than 12 triclinic correction vectors, ignoring some. > > There is probably something wrong with your box. > > 0.0e+00, 0.0e+00} > > 3.89470e-01, 2.50360e+00 3.41610e-01 Box[1]={ > 3.41610e-01, 5.49000e-03, 5.26833e+00} > > 2.91510e+00 Box (3x3): > > 2.91510e+00, , 0.0e+00} > >Box[1]={ Box[0]={ 0.0e+00 2.50360e+00 > 5.49000e-03, > > > > I checked the .gro file to see the unit cell vectors are listed > correctly. > > > > The protein has the following sides and angles: > > > > a = 25.04, b = 29.41, c = 52.79, α = 89.45, β = 86.29, γ = 82.39 > > > > and I calculate the unit vectors to be: > > > > a = [ 25.036, 0. , 0. ] > > b = [ 3.8947483 , 29.15096972, 0.] > > c = [ 3.41611372, 0.05486764, 52.6816] > > > > and the .gro file has the line: > > > > 2.50360 2.91510 5.26833 0.0 0.0 0.38947 0.0 > 0.34161 0.00549 > > > > which seems to be correct. > > > > I have also verified that the conditions 3.1-3.3 listed on page 12 on > the manual for 5.1 to be correct. > > > > What could be the problem? > > > > Best, > > Irem > > -- > > 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.
Re: [gmx-users] Inconsistent shifts
Hi, I wouldn't worry about that warning from gmx traj. It's probably relevant in some other context, but somebody wrote some dirty code that got re-used in a context they did not intend. Mark On Tue, Mar 8, 2016 at 5:08 PM Jan Meyer wrote: > > Dear gmx users, > > i am using gmx 5.0.5 and i have a question concerning the error "There > were x inconsistent shifts. Check your topology". > I read some older posts about this error and do know that it comes together > with something beeing wrong in the handling of pbc. I want to mention > at the beginning > that i have set "periodic-molecules = yes" in the mdp-file. > > My initial system consists of polyisoprene chains that contain up > to 200 Monomer units. The system size is roughly 10x10x20 nm^3. > It can be simulated (NPT) without any issues in parallel on 48 cores. > Between the polymerchains i want to add sulfur bridges containing 2 sulfur > atoms each. I am also able to stable run this system but when I use > g_traj i get the above mentioned warning/error. > > I have also used the debug tool for g_traj to get more information. > It said: > "Guessed pbc = xyz from the box matrix > mk_grey: shifts for atom 93303 due to atom 93302 > are (1,2,0), should be (2,1,0) > dx = (-0.177,0.106,0.0096)" > > From the source code i tried to understand how these shifts are > calculated. > But so far i did not suceed. Is there maybe someone who can explain it > in detail? > > I hope i could clearly explain my problem. If thats not the case and > more information > is needed please contact me. > > > Thanks in advance > Jan > > -- > 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.
Re: [gmx-users] unit cell vector warning
Hi, I'm generating the box from the.pdb file with pdb2gmx. The protein in question is 5e1k. I do the simulations in the protein unit cell. Best, Irem > On Mar 8, 2016, at 11:39 AM, Mark Abraham wrote: > > Hi, > > How are you actually generating the coordinate file, and/or the box > vectors? As far as I know, nobody's written down the set of vectors that > should work sensibly, but it's likely that the gmx tools will write boxes > that will definitely work later on... > > Mark > >> On Tue, Mar 8, 2016 at 4:27 PM Irem Altan wrote: >> >> Hi, >> >> An update on the unit cell problem: when I make small changes in the >> angle, say change 89.45 to 89.00, the error disappears. I’m still getting >> the same warning. This is with version 5.1.2. Could this be a numerical >> precision issue (c_y is 0.05, see below) or a bug? I tried to run this >> without the protein, by just putting water and a few ions in the box. >> >> Best, >> Irem >> >>> On Mar 3, 2016, at 4:15 PM, Irem Altan wrote: >>> >>> Hi, >>> >>> I am trying to simulate a protein in its triclinic unit cell. During the >> energy minimization and MD simulation, GROMACS prints the following out at >> every step: >>> >>> WARNING: Found more than 12 triclinic correction vectors, ignoring some. >>> There is probably something wrong with your box. >>> 0.0e+00, 0.0e+00} >>> 3.89470e-01, 2.50360e+00 3.41610e-01 Box[1]={ >> 3.41610e-01, 5.49000e-03, 5.26833e+00} >>> 2.91510e+00 Box (3x3): >>> 2.91510e+00, , 0.0e+00} >>> Box[1]={ Box[0]={ 0.0e+00 2.50360e+00 >> 5.49000e-03, >>> >>> I checked the .gro file to see the unit cell vectors are listed >> correctly. >>> >>> The protein has the following sides and angles: >>> >>> a = 25.04, b = 29.41, c = 52.79, α = 89.45, β = 86.29, γ = 82.39 >>> >>> and I calculate the unit vectors to be: >>> >>> a = [ 25.036, 0. , 0. ] >>> b = [ 3.8947483 , 29.15096972, 0.] >>> c = [ 3.41611372, 0.05486764, 52.6816] >>> >>> and the .gro file has the line: >>> >>> 2.50360 2.91510 5.26833 0.0 0.0 0.38947 0.0 >> 0.34161 0.00549 >>> >>> which seems to be correct. >>> >>> I have also verified that the conditions 3.1-3.3 listed on page 12 on >> the manual for 5.1 to be correct. >>> >>> What could be the problem? >>> >>> Best, >>> Irem >>> -- >>> 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.
Re: [gmx-users] Details of 5.0 benchmark report?
Hi, What details are you interested in? IIRC the inputs are clearly specified (although perhaps not provided there). -- Szilárd On Fri, Mar 4, 2016 at 5:15 PM, Adam Huffman wrote: > Hello > > Are details of the running of the benchmarks reported for version 5.0 > available anywhere? > > I'm referring to the report published at: > > http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf > > I would like to be able to run these myself, on three different systems. > > > Cheers, > Adam > -- > 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] apply force on single molecule
Dear all, I want look at change in potential energy profile, when i apply force on a molecule on one end where other end fixed in a position. Is it possible do it in gromacs. If yes, how may i proceed? --Masrul -- 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] apply force on single molecule
Yes. Take a look at the manual for information on using the Pulling code. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Parvez Mh Sent: Tuesday, March 08, 2016 2:20 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] apply force on single molecule Dear all, I want look at change in potential energy profile, when i apply force on a molecule on one end where other end fixed in a position. Is it possible do it in gromacs. If yes, how may i proceed? --Masrul -- 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.
Re: [gmx-users] fix COM
Thank you Justin, The flat-bottom position restraint fixed my problem indeed. -- 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] Neutralizing
On 3/8/16 3:59 AM, mohammad r wrote: Thank you Parham You mean that it is not necessary to do QM/MM simulation? The trivial task of adding ions to neutralize the net charge on the system certainly does not require anything like QM/MM. -Justin On Tuesday, March 8, 2016 11:13 AM, Parham Jabbarzadeh (Department of Biomedical Science) wrote: Dear Sir Use this command: gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral In this case, you don't need the number of ions. Kind Regards Parham J. K. ===== PhD candidate - Lecturer in drug discovery Faculty of Medicine and Health SciencesUniversity Putra MalaysiaMalaysia =====Publication ::: Featured Publication ::: Website ::: FaceBook On Tue, Mar 8, 2016 at 3:32 PM, mohammad r wrote: Hi everybody, I’ve generated a water-peptide system, now I want to neutralize it. Is adding adequate number of ions sufficient for neutralizing process or I should do QM/MM simulation for the this process? Thank you, Mohammad. -- 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. -- == 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.
Re: [gmx-users] distance restraints in mdp
On 3/7/16 10:35 PM, Sana Saeed wrote: i am performing protein ligand binding free energy calculation MD. i have applied distance restraint to 1 pair of atoms. now when i am running md it gives me LINCS warnings. first i thought it is because of wrong geometry so i changed complex, now i am doing it for Lysozyme+JZ4. but still same warning. i am confused about the distance restraints to be introduced in mdp file. disre = simple/ensemble? i read in manual, but still confused. i tried both with "simple it gives me LINCS warning and with ensemble it says that this version of gromacs doesnt support it. i am using 5.1 gromacs. Then simplify further and make sure the system runs without restraints or anything else. Just normal MD. Start simple to avoid chasing the wrong problem. -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.
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 35
dear Justin Lemkuli already run that without restraints, it has no problems. even i used the gro file from the simple 5ns MD but still have these same errors and warnings. when i set Lincs constraints to all-bonds , simulation finishes fine but by using alchemical_analysis.py for free energies it gives errors and warnings. (Warning: states 29 and 37 have the same energies on the dataset.) i used 42 lambdas and about 32 states are having same energies. and when i set constraints to h-bonds then LINCS warnings. i tried to use different options for pressure coupling also because i read somewhere it also affects simulation. i am quite confused where the problem is. is it possible to send you topology file and you have a look?Thanks in advance Sana Saeed Khan,Teaching-Research AssistantChemoinformatics LabGraduate Student, MS bioinfoDepartment of BioinformaticsSoongsil University, Seoul, South Korea. On Wednesday, March 9, 2016 9:58 AM, "gromacs.org_gmx-users-requ...@maillist.sys.kth.se" wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than "Re: Contents of gromacs.org_gmx-users digest..." Today's Topics: 1. Re: Details of 5.0 benchmark report? (Szil?rd P?ll) 2. apply force on single molecule (Parvez Mh) 3. Re: apply force on single molecule (Smith, Micholas D.) 4. Re: fix COM (Ming Tang) 5. Re: Neutralizing (Justin Lemkul) 6. Re: distance restraints in mdp (Justin Lemkul) -- Message: 1 Date: Tue, 8 Mar 2016 18:08:20 +0100 From: Szil?rd P?ll To: Discussion list for GROMACS users Subject: Re: [gmx-users] Details of 5.0 benchmark report? Message-ID: Content-Type: text/plain; charset=UTF-8 Hi, What details are you interested in? IIRC the inputs are clearly specified (although perhaps not provided there). -- Szil?rd On Fri, Mar 4, 2016 at 5:15 PM, Adam Huffman wrote: > Hello > > Are details of the running of the benchmarks reported for version 5.0 > available anywhere? > > I'm referring to the report published at: > > http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf > > I would like to be able to run these myself, on three different systems. > > > Cheers, > Adam > -- > 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. > -- Message: 2 Date: Tue, 8 Mar 2016 13:20:49 -0600 From: Parvez Mh To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] apply force on single molecule Message-ID: Content-Type: text/plain; charset=UTF-8 Dear all, I want look at change in potential energy profile, when i apply force on a molecule on one end where other end fixed in a position. Is it possible do it in gromacs. If yes, how may i proceed? --Masrul -- Message: 3 Date: Tue, 8 Mar 2016 19:29:54 + From: "Smith, Micholas D." To: "gmx-us...@gromacs.org" Subject: Re: [gmx-users] apply force on single molecule Message-ID: <1457465394988.73...@ornl.gov> Content-Type: text/plain; charset="iso-8859-1" Yes. Take a look at the manual for information on using the Pulling code. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Parvez Mh Sent: Tuesday, March 08, 2016 2:20 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] apply force on single molecule Dear all, I want look at change in potential energy profile, when i apply force on a molecule on one end where other end fixed in a position. Is it possible do it in gromacs. If yes, how may i proceed? --Masrul -- 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. -- Message: 4 Date: Wed, 9 Mar 2016 00:21:50 + From
Re: [gmx-users] distance restraints in mdp
Please don't reply to the entire digest. Copy the relevant portions and use a proper subject line. On 3/8/16 8:19 PM, Sana Saeed wrote: dear Justin Lemkuli already run that without restraints, it has no problems. even i used the gro file from the simple 5ns MD but still have these same errors and warnings. when i set Lincs constraints to all-bonds , simulation finishes fine but by using alchemical_analysis.py for free energies it gives errors and warnings. (Warning: states 29 and 37 have the same energies on the dataset.) i used 42 lambdas and about 32 states are having same energies. and when i set constraints to h-bonds then LINCS warnings. i tried to use different options for pressure coupling also because i read somewhere it also affects simulation. i am quite confused where the problem is. is it possible to send you topology file and you have a look?Thanks in advance Now we're talking about half a million different things. When reporting a problem, please keep it simple. It's impossible for anyone on this mailing list to be inside your head and know what you've done. If you want to troubleshoot distance restraints, we can do that. But let's take things one at a time. If you want to share files, please upload a tarball of *all* input files: coordinates, topology(ies), any relevant .mdp file(s), and a run script that lists all of your commands, exactly in sequence as you typed them. Please do not send this information privately; share with the list so others can contribute (I'm frankly swamped lately and have little time to delve deeply into such issues but I'll try to make a little time). -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.
Re: [gmx-users] Neutralizing
Thank you Parham and Justin, Excuse me I have another question, in simulation of a water-peptide system, is it necessary to use QM/MM simulation during the entire process? Because I didn't see it in the tutorials. By the way I generated the pdb file by using charmm-gui then import it in amber to get the topology and coordinate files, finally I converted the topology and coordinate files to gromacs format and did the rest of simulation by gromacs. but I didn't run QM/MM simulation. Does it make trouble in the results? Best, Mohammad. On Wednesday, March 9, 2016 4:26 AM, Justin Lemkul wrote: On 3/8/16 3:59 AM, mohammad r wrote: > Thank you Parham > You mean that it is not necessary to do QM/MM simulation? > The trivial task of adding ions to neutralize the net charge on the system certainly does not require anything like QM/MM. -Justin > On Tuesday, March 8, 2016 11:13 AM, Parham Jabbarzadeh (Department of >Biomedical Science) wrote: > > > Dear Sir > > Use this command: > > gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral > > In this case, you don't need the number of ions. > Kind Regards > > Parham J. K. > ===== > PhD candidate - Lecturer in drug discovery > Faculty of Medicine and Health SciencesUniversity Putra MalaysiaMalaysia > =====Publication ::: Featured Publication ::: Website > ::: FaceBook > On Tue, Mar 8, 2016 at 3:32 PM, mohammad r wrote: > > Hi everybody, I’ve generated a water-peptide system, now I want to neutralize > it. Is adding adequate number of ions sufficient for neutralizing process or > I should do QM/MM simulation for the this process? Thank you, Mohammad. > -- > 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. > > > > > -- == 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.