Re: [gmx-users] energy minimization problem
On 11/3/13 6:20 AM, kiana moghaddam wrote: Dear Justin Further to your previous email, I want to calculate free energy for DNA-ligand interaction. According to your answer, for more sensitive calculations like free energy simulations and normal modes, emtolshould be lower than 1. As I understand, you mean that for these systems emtol should be 0 or negative. Is it really true? No. You are not likely to ever achieve zero force, and a negative value is impossible. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] energy minimization problem
Hi GMX Users I 'm running MD Simulation for DNA-ligand interaction. I ran energy minimization with emtol=10, 100 and 250 in 1 steps (steepest descent followed by the conjugate gradient algorithm). The lowest value for energy obtained for emtol=10. I have some questions about energy minimization step. what is suitable value for emtol in em.mdp file? how many steps is needed for energy minimization? and how do I understand the minimization is successful? Best Regards Kiana -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] energy minimization problem
On 11/2/13 3:38 PM, kiana moghaddam wrote: Hi GMX Users I 'm running MD Simulation for DNA-ligand interaction. I ran energy minimization with emtol=10, 100 and 250 in 1 steps (steepest descent followed by the conjugate gradient algorithm). The lowest value for energy obtained for emtol=10. I have some questions about energy minimization step. what is suitable value for emtol in em.mdp file? how many steps is needed for energy minimization? and how do I understand the minimization is successful? The purpose of EM is to generate a reasonable configuration that can be subjected to dynamics. For most standard MD, an emtol in the neighborhood of 100-1000 is sufficient, and there are no hard and fast rules that I know of that motivates that choice. If MD fails, run EM again with a lower tolerance. For more sensitive calculations like free energy simulations and normal modes, you will want to minimize much more thoroughly (for NM, emtol 1) and in double precision. As long as the potential energy is negative and in a range that is expected given the size of the system (10^5 - 10^6 in the case of most solvated proteins or membranes), the outcome is probably acceptable. The number of steps is largely irrelevant; the energetic outcome is far more important. I usually set nsteps to some huge value and just let EM converge as far as it will. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] energy minimization problem
Hi , I have a protein with 2 chains. I need to do normal mode analysis on it. As there are no covalent bonds between the two chains, I did not use the merge option in the pdb2gmx command. I am trying to energy minimize the structure , in vaccum.( in double precision) , but am not able to get the Fmax below e-02. i have tried using the l-bgs minimization technique. The lbfgs.mdp file is as follows define = -DFLEXIBLE constraints = none integrator = l-bfgs tinit= 0 nsteps = 1 nbfgscorr= 10 emtol= .001 emstep = 0.5 gen_vel = no gen-temp = 300 nstcomm = 1 ns_type = grid rlist= 1.2 rcoulomb = 1.2 rvdw = 1.0 Tcoupl = no Pcoupl = no coulombtype = PME vdwtype = shift The minimization continues up to the specified no. of steps. When I try to give another minimization run on the minimized structure, the Fmax goes upto the order e+00. I am not being able to figure out the problem. Any suggestion regarding this will be very helpful. Thanks in advance Sarbani. -- 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] energy minimization problem
Actual text input / output would be a good idea here. What is the actual output when you try to run it the second time? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of sarbani chattopadhyay Sent: Friday, 26 February 2010 12:06 AM To: gmx-users@gromacs.org Subject: [gmx-users] energy minimization problem Hi , I have a protein with 2 chains. I need to do normal mode analysis on it. As there are no covalent bonds between the two chains, I did not use the merge option in the pdb2gmx command. I am trying to energy minimize the structure , in vaccum.( in double precision) , but am not able to get the Fmax below e-02. i have tried using the l-bgs minimization technique. The lbfgs.mdp file is as follows define = -DFLEXIBLE constraints = none integrator = l-bfgs tinit = 0 nsteps = 1 nbfgscorr = 10 emtol = .001 emstep = 0.5 gen_vel = no gen-temp = 300 nstcomm = 1 ns_type = grid rlist = 1.2 rcoulomb = 1.2 rvdw = 1.0 Tcoupl = no Pcoupl = no coulombtype = PME vdwtype = shift The minimization continues up to the specified no. of steps. When I try to give another minimization run on the minimized structure, the Fmax goes upto the order e+00. I am not being able to figure out the problem. Any suggestion regarding this will be very helpful. Thanks in advance Sarbani. http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline@middle? ~WRD000.jpg-- 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] Energy minimization problem with Double precision and mpi
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Sunday, June 24, 2007 4:18 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah Zayner wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:gmx-users- [EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, June 23, 2007 4:36 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah Zayner wrote: I managed to install mdrun_d from CVS and the problem is fixed you didn't say which cvs solved your problem. was it the release_3_3_patches branch? Mdrun_d says version: 3.3.99_development_20070413 It was the main branch. OK, this branch is not yet quite stable, we are still testing things there. It would be good to know whether the release_3_3_patches branch also solves your problem. Installing the release-3-3-patches branch also solves the problem. I only tested it on two nodes ie. -np 2 but I assume it would also work for more. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy minimization problem with Double precision and mpi
Josiah Zayner wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Sunday, June 24, 2007 4:18 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah Zayner wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:gmx-users- [EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, June 23, 2007 4:36 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah Zayner wrote: I managed to install mdrun_d from CVS and the problem is fixed you didn't say which cvs solved your problem. was it the release_3_3_patches branch? Mdrun_d says version: 3.3.99_development_20070413 It was the main branch. OK, this branch is not yet quite stable, we are still testing things there. It would be good to know whether the release_3_3_patches branch also solves your problem. Installing the release-3-3-patches branch also solves the problem. I only tested it on two nodes ie. -np 2 but I assume it would also work for more. Thanks, that is good to hear. It could be due to parallel minimization, but if it is fixed in CVS I won't investigate it further. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Energy minimization problem with Double precision and mpi
I managed to install mdrun_d from CVS and the problem is fixed -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Josiah Zayner Sent: Saturday, June 23, 2007 1:05 PM To: gmx-users@gromacs.org Subject: [gmx-users] Energy minimization problem with Double precision and mpi Each time I try to run mdrun with double precision and more than one node, I always receive some atom with infinite Fmax, no matter what I do, Always on Step=0. The strangest thing is that it still attempts the minimization but the values never change except for Dmax in a steepest descent. If I change the coordinates of the atom that has the inf value another one has infinite value and so on. I use lam/mpi, with the command 'mpirun -np 5 mdrun_d -v -deffnm potd'. My double precision was configured with both --enable-mpi and --enable-double. Here is a copy of the mdp file I use: title = potd cpp = /usr/bin/cpp constraints = none integrator = steep nsteps = 0 ns_type = grid nstcomm = 1 nstlist = 10 rlist = 1.4 coulombtype = Shift vdw_type= Shift rcoulomb= 1.2 rvdw= 1.2 rcoulomb_switch = 1.0 rvdw_switch = 1.0 epsilon_r = 6.0 optimize_fft= yes emtol = 1000 emstep = 0.01 nstcgsteep = 100 It doesn't matter if it is in vaccum or water. I have minimized to an emtol of 10 and mdrun_d still does not work. I am using gromacs 3.3.1. I have tried changing or removing almost every value in the mdp file. I have tried different pdb files. Tried using grompp and grompp_d. Tried with -sort -shuffle and without. Is this another one of those compiler issues like genion? Any help would be great. Thanks, Josiah Zayner ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Energy minimization problem with Double precision and mpi
Each time I try to run mdrun with double precision and more than one node, I always receive some atom with infinite Fmax, no matter what I do, Always on Step=0. The strangest thing is that it still attempts the minimization but the values never change except for Dmax in a steepest descent. If I change the coordinates of the atom that has the inf value another one has infinite value and so on. I use lam/mpi, with the command 'mpirun -np 5 mdrun_d -v -deffnm potd'. My double precision was configured with both --enable-mpi and --enable-double. Here is a copy of the mdp file I use: title = potd cpp = /usr/bin/cpp constraints = none integrator = steep nsteps = 0 ns_type = grid nstcomm = 1 nstlist = 10 rlist = 1.4 coulombtype = Shift vdw_type= Shift rcoulomb= 1.2 rvdw= 1.2 rcoulomb_switch = 1.0 rvdw_switch = 1.0 epsilon_r = 6.0 optimize_fft= yes emtol = 1000 emstep = 0.01 nstcgsteep = 100 It doesn't matter if it is in vaccum or water. I have minimized to an emtol of 10 and mdrun_d still does not work. I am using gromacs 3.3.1. I have tried changing or removing almost every value in the mdp file. I have tried different pdb files. Tried using grompp and grompp_d. Tried with -sort -shuffle and without. Is this another one of those compiler issues like genion? Any help would be great. Thanks, Josiah Zayner ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Energy minimization problem with Double precision and mpi
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, June 23, 2007 4:36 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah Zayner wrote: I managed to install mdrun_d from CVS and the problem is fixed you didn't say which cvs solved your problem. was it the release_3_3_patches branch? Mdrun_d says version: 3.3.99_development_20070413 It was the main branch. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Josiah Zayner Sent: Saturday, June 23, 2007 1:05 PM To: gmx-users@gromacs.org Subject: [gmx-users] Energy minimization problem with Double precision and mpi Each time I try to run mdrun with double precision and more than one node, I always receive some atom with infinite Fmax, no matter what I do, Always on Step=0. The strangest thing is that it still attempts the minimization but the values never change except for Dmax in a steepest descent. If I change the coordinates of the atom that has the inf value another one has infinite value and so on. I use lam/mpi, with the command 'mpirun -np 5 mdrun_d -v -deffnm potd'. My double precision was configured with both --enable-mpi and --enable-double. Here is a copy of the mdp file I use: title = potd cpp = /usr/bin/cpp constraints = none integrator= steep nsteps= 0 ns_type = grid nstcomm = 1 nstlist = 10 rlist = 1.4 coulombtype = Shift vdw_type = Shift rcoulomb = 1.2 rvdw = 1.2 rcoulomb_switch = 1.0 rvdw_switch = 1.0 epsilon_r = 6.0 optimize_fft = yes emtol = 1000 emstep= 0.01 nstcgsteep= 100 It doesn't matter if it is in vaccum or water. I have minimized to an emtol of 10 and mdrun_d still does not work. I am using gromacs 3.3.1. I have tried changing or removing almost every value in the mdp file. I have tried different pdb files. Tried using grompp and grompp_d. Tried with -sort -shuffle and without. Is this another one of those compiler issues like genion? Any help would be great. Thanks, Josiah Zayner ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)
Dear gmx-users: I am trying to simulate a surfactant-water system(also contains some co-surfactants). Surfactant is a cationic surfactant with chloride as counterion. And the cosurfactant is fatty alcohol. water is of spc model. I got topologies from Prodrg for my surfactant and cosurfactant. So I minimized the energies for both my molecules. And prepared a system of 1400 waters, 20 surfactants, 20 counter ions and 40 cosurfactants in a box of 5X5X8 nm^3 using packmol. I tried to minimize the energy of the system using l-bfgs. But I am always getting the error attached below. In my em.mdp file I am using pme for coulomb type. Even for MDRUN also I am getting the same error... I checked the previous posts and I am unable to understand what's the problem. And can anyone tell what is meant by broken topology??? Also try to help me to get out of the problem. Low-Memory BFGS Minimizer: Tolerance (Fmax) = 2.0e+04 Number of steps=1 Warning: 1-4 interaction between 1 and 4 at distance 3.540 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Using 10 BFGS correction steps. F-max = inf on atom 97 F-Norm= nan --- My topology contains a system of four types surfactant, cosurfctant, water and Chloride ions. Until grompp everything is fine. Total charge on system is zero. I can give any more details if it is needed. -- Arun kumar.V M.E Chemical ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)
Hi Arun, You have to get your methods straight.., and be more clear in the phrasing of your question. I am trying to simulate a surfactant-water system(also contains some co-surfactants). Surfactant is a cationic surfactant with chloride as counterion. And the cosurfactant is fatty alcohol. water is of spc model. I got topologies from Prodrg for my surfactant and cosurfactant. What force field do you use? The standard output from PRODRG for gromacs is the gmx force field, which is deprecated and shouldn't be used (this is in the archives). So I minimized the energies for both my molecules. And prepared a system of 1400 waters, 20 surfactants, 20 counter ions and 40 cosurfactants in a box of 5X5X8 nm^3 using packmol. Maybe you're better of trying one surfactant molecule and one chloride in water to start with? I tried to minimize the energy of the system using l-bfgs. But I am always getting the error attached below. In my em.mdp file I am using pme for coulomb type. Even for MDRUN also I am getting the same error... I checked the previous posts and I am unable to understand what's the problem. And can anyone tell what is meant by broken topology??? Also try to help me to get out of the problem. Even for MDRUN? pfff, that must be really bad then. First of all, do you mean running the program 'mdrun' with the .tpr file for l-bfgs EM, or an actual MD run? In case of the latter, wouldn't you think there's little point in starting an MD run if energy minimization already failed? In case of the former, the statement is redundant (now it's just confusing). F-max = inf on atom 97 F-Norm= nan --- So, your system is exploding... Do you have any overlapping bonds/atoms? Does your box actually contain your system? (Do think periodically..., overlapping periodic images?). My topology contains a system of four types surfactant, cosurfctant, water and Chloride ions. Until grompp everything is fine. Total charge on system is zero. I can give any more details if it is needed. Good, until grompp everything's fine. Now, then the error comes as a surprise! But what did you do before? What steps did you take? Oh, and I bet that in your .mdp file it says tc-grps = SOL SUR ALC CL, albeit that the actual names and the order of them may be different. This is an issue, which has also been dealt with extensively (including the past week). In any case, when reporting that you've ran into a problem, it may be helpful to us to send your .mdp file. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy Minimization problem
19 apr 2007 kl. 03.45 skrev Venky Krishna: Hi George, I usually delete/move the molecules reported to have high force values in the minimization steps. A better thing would be to start with a box which has sufficient intermolecular distance again by deleting molecules which are very close to each other (use the g_mindist program) and then energy minimize the system. Btw...did you define FLEXIBLE for water molecules during your em runs? Best Venky On Apr 18, 2007, at 5:24 PM, George Abadir wrote: Hi, I am doing an energy minimization for a carbon nanotube (end capped with hydrogen atoms) in a box of water. I get the following message: 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 altogether (set constraints = none in mdp file) Steepest Descents converged to machine precision in 1836 steps, but did not reach the requested Fmax 10. Potential Energy = -2.4277438+06 Maximum force = 5.9858018+03 on atom 13 Norm of force = 5.1364398+04 The potential energy is extremely low and the maximum force is considerably large. I turned off the constrained and tried other energy minimization methods but still got the same error (with different magnitudes of the force and energy of course). Is it likely that double precision simulation can make such a big difference? If not (which I think) is there any other way to solve the problem? I wouldn't call this an error. The minimization converged, and your potential energy is low. There is no problem to solve. /Erik Thank you very much in advance, George Abadir ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy Minimization problem
Thanks guys for your replies. The problem is that the potential energy is too low: it can't be true I think. Also, the high force means that the system is not really stable (at least the atom influenced by this force is not!). And yes I defined flexible for the water molecules. I don't know if there is another solution other than deleting the atom influenced by the large force, because if I delete it I'll be changing my system which I would rather not do. Any help is much appreciated, Thanks alot, George Erik Marklund wrote: 19 apr 2007 kl. 03.45 skrev Venky Krishna: Hi George, I usually delete/move the molecules reported to have high force values in the minimization steps. A better thing would be to start with a box which has sufficient intermolecular distance again by deleting molecules which are very close to each other (use the g_mindist program) and then energy minimize the system. Btw...did you define FLEXIBLE for water molecules during your em runs? Best Venky On Apr 18, 2007, at 5:24 PM, George Abadir wrote: Hi, I am doing an energy minimization for a carbon nanotube (end capped with hydrogen atoms) in a box of water. I get the following message: 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 altogether (set constraints = none in mdp file) Steepest Descents converged to machine precision in 1836 steps, but did not reach the requested Fmax 10. Potential Energy = -2.4277438+06 Maximum force = 5.9858018+03 on atom 13 Norm of force = 5.1364398+04 The potential energy is extremely low and the maximum force is considerably large. I turned off the constrained and tried other energy minimization methods but still got the same error (with different magnitudes of the force and energy of course). Is it likely that double precision simulation can make such a big difference? If not (which I think) is there any other way to solve the problem? I wouldn't call this an error. The minimization converged, and your potential energy is low. There is no problem to solve. /Erik Thank you very much in advance, George Abadir ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy Minimization problem
George Abadir wrote: Thanks guys for your replies. The problem is that the potential energy is too low: it can't be true I think. Also, the high force means that the system is not really stable (at least the atom influenced by this force is not!). And yes I defined flexible for the water molecules. I don't know if there is another solution other than deleting the atom influenced by the large force, because if I delete it I'll be changing my system which I would rather not do. Well without knowing why you think this energy is too low and this force too high, we can't say much else, other than to suggest your check your topology. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Energy Minimization problem
Hi, I am doing an energy minimization for a carbon nanotube (end capped with hydrogen atoms) in a box of water. I get the following message: 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 altogether (set constraints = none in mdp file) Steepest Descents converged to machine precision in 1836 steps, but did not reach the requested Fmax 10. Potential Energy = -2.4277438+06 Maximum force = 5.9858018+03 on atom 13 Norm of force = 5.1364398+04 The potential energy is extremely low and the maximum force is considerably large. I turned off the constrained and tried other energy minimization methods but still got the same error (with different magnitudes of the force and energy of course). Is it likely that double precision simulation can make such a big difference? If not (which I think) is there any other way to solve the problem? Thank you very much in advance, George Abadir ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy Minimization problem
Hi George, I usually delete/move the molecules reported to have high force values in the minimization steps. A better thing would be to start with a box which has sufficient intermolecular distance again by deleting molecules which are very close to each other (use the g_mindist program) and then energy minimize the system. Btw...did you define FLEXIBLE for water molecules during your em runs? Best Venky On Apr 18, 2007, at 5:24 PM, George Abadir wrote: Hi, I am doing an energy minimization for a carbon nanotube (end capped with hydrogen atoms) in a box of water. I get the following message: 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 altogether (set constraints = none in mdp file) Steepest Descents converged to machine precision in 1836 steps, but did not reach the requested Fmax 10. Potential Energy = -2.4277438+06 Maximum force = 5.9858018+03 on atom 13 Norm of force = 5.1364398+04 The potential energy is extremely low and the maximum force is considerably large. I turned off the constrained and tried other energy minimization methods but still got the same error (with different magnitudes of the force and energy of course). Is it likely that double precision simulation can make such a big difference? If not (which I think) is there any other way to solve the problem? Thank you very much in advance, George Abadir ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Energy Minimization Problem
On Mon, 17 Apr 2006 08:21:35 -0400 (EDT) Robson P. S. Peguin [EMAIL PROTECTED] wrote: Hi everybody, I'm trying to simulate an interfacial system using Gromacs. My simulation box has water in one side and hydrofluorocarbon in the other side. This system was successfully tested using DL-POLY simulation package previously. Also, the box containing pure hydrofluorocarbon worked fine using Gromacs. However, when I try an energy minimization simulation with the interfacial system, after a couple of steps (~400), the geometry of the hydrofluorocarbon changes. I mean, the molecules begin to lose bonds or atoms. It didn't collapse the box yet, but I can see from a visualization package that the molecules are distorted. I tried to decrease the timestep unsuccessfully. If you have any suggestions, I'll be happy to know them. You should check your topology: bond definition from what you describe lokks necessary. XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
