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
[gmx-users] Energetics in collision
Hello gmx-users! I am studying the effect of impact velocity of a water droplet in collision with a frozen surface in NVE ensemble. A droplet has extra translational energy, which corresponds to a specific velocity, in addition to thermal energy at 300K. I supposed that at the collision extra translational energy of the droplet will change to potential and kinetic energy of the droplet so that total energy of the system is conserved. However, even I observe increase in potential and kinetic energy, total energy of the system (~300 000kJ/mol) first decreases slightly (100kJ - exact value depends on the velocity) and just after that reverts partly, but stabilizes value lower than at the beginning. The total energy should be conserved but on the other hand it sounds logical that there will be stabilizing energy from the droplet-surface interactions which prevents the droplet to bounce away and makes it to equilibrate on the surface. I am wondering if this is the case or have I done some mistake which disturbs the energy conservation? The other question concerns about the intrusion of the droplet into the pores of the structured surface. The situation is otherwise the same but now the total energy continues to decrease after first touch and wont stabilize until the bottom of the pore is reached. It again sounds like a consequence of the stabilizing energy from the droplet-surface interactions, but now when these interactions are larger than without the intrusion also slight increase (2-3K) in the droplet temperature is observed. It sounds little bit strange that water molecules in the pores would have higher temperature. So again is it really the truth or have I done something what I shouldnt have? Thanks for your time and assistance, Janne ___ 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] Re: Energetics in collision
First thanks for your reply! Hello gmx-users! I am studying the effect of impact velocity of a water droplet in collision with a frozen surface in NVE ensemble. A droplet has extra translational energy,which corresponds to a specific velocity, in addition to thermal energy at 300K. I supposed that at the collision extra translational energy of the droplet will change to potential and kinetic energy of the droplet so that total energy of the system is conserved. However, even I observe increase in potential and kinetic energy, total energy of the system (~300 000kJ/mol) first decreases slightly (100kJ - exact value depends on the velocity) and just after that reverts partly, but stabilizes value lower than at the beginning. Don't know for sure, but incorrect comm removal springs to mind. I wont remove COM motion so that translational velocity is not disturbed. The total energy should be conserved but on the other hand it sounds logical that there will be stabilizing energy from the droplet-surface interactions which prevents the droplet to bounce away and makes it to equilibrate on the surface. I am wondering if this is the case or have I done some mistake which disturbs the energy conservation? Wouldn't that stabilizing energy be part of the total energy? That sounds realistic but I just tried to figure out some reason for decreased total energy, which actually in case of porous surface decrease little by little while water molecules intrude the pores and stabilize just after the bottom of the pores is reached. Then it should be so that extra stabilization from droplet-surface interactions in potential energy would be equally out of water-water interactions if temperature wont change. In that case what makes the droplet stay on surface with specific contact angle? Now I am so confused that I dont know anything - hopefully someone can explain it to me... The other question concerns about the intrusion of the droplet into the pores of the structured surface. The situation is otherwise the same but now the total energy continues to decrease after first touch and wont stabilize until the bottom of the pore is reached. It again sounds like a consequence of the stabilizing energy from the droplet-surface interactions, but now when these interactions are larger than without the intrusion also slight increase (2-3K) in the droplet temperature is observed. It sounds little bit strange that water molecules in the pores would have higher temperature. So again is it really the truth or have I done something what I shouldnt have? Thanks for your time and assistance, Janne ___ 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] do_dssp crashes on certain machines..
Dear community, I have the following problem with do_dssp, when I try analysing a long 70 ns trajectory produced by a REMD calculation. All my previous analysis went fine, when the trajectory had a length of ~= 50ns. However, I now obtain the following errror message, perhaps one hour after launching do_dssp, when the standard error message says frames around 54ns are being analysed: Group12 ( Cl) has 8 elements Group13 ( SOL) has 42228 elements Group14 ( Other) has 42236 elements Select a group: There are 103 residues in your selected group Opening library file /home/coutinho/software/gromacs-3.3.0/icc9.0/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up ddKGQneH to ./#ddKGQneH.1# Reading frame 36630 time 54945.000 --- Program do_dssp, VERSION 3.3 Source code file: futil.c, line: 340 File input/output error: ddr3C7fs --- I guess this problem is due to the architecture/memory of the nodes of the cluster I use (where this error occurs whether do_dssp is the only job on the node or not): The same analysis works fine on another machine. The cluster I use is made of Hewlett-Packard ProLiant DL145 G2 AMD Opteron Model 246 nodes. The nodes contain two AMD opteron 2.4GHz cpus and 4*1GB memory. I thank you very much for any suggestions! Pascal Baillod *** Pascal Baillod (PhD student) *** Swiss Federal Institute of Technology EPFL Tel: +41-(0)21-693-0322 Institute of Chemical Sciences and Engineering ,Fax: +41-(0)21-693-0320 Laboratory of Computational Chemistry and Biochemistry [EMAIL PROTECTED] Room BCH 4121, Avenue Forel,http://lcbcpc21.epfl.ch CH-1015 Lausanne *** ___ 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] do_dssp crashes on certain machines..
[EMAIL PROTECTED] wrote: Dear community, I have the following problem with do_dssp, when I try analysing a long 70 ns trajectory produced by a REMD calculation. All my previous analysis went fine, when the trajectory had a length of ~= 50ns. However, I now obtain the following errror message, perhaps one hour after launching do_dssp, when the standard error message says frames around 54ns are being analysed: Group12 ( Cl) has 8 elements Group13 ( SOL) has 42228 elements Group14 ( Other) has 42236 elements Select a group: There are 103 residues in your selected group Opening library file /home/coutinho/software/gromacs-3.3.0/icc9.0/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up ddKGQneH to ./#ddKGQneH.1# Reading frame 36630 time 54945.000 --- Program do_dssp, VERSION 3.3 Source code file: futil.c, line: 340 File input/output error: ddr3C7fs --- I guess this problem is due to the architecture/memory of the nodes of the cluster I use (where this error occurs whether do_dssp is the only job on the node or not): The same analysis works fine on another machine. The cluster I use is made of Hewlett-Packard ProLiant DL145 G2 AMD Opteron Model 246 nodes. The nodes contain two AMD opteron 2.4GHz cpus and 4*1GB memory. I thank you very much for any suggestions! Do the analysis piecewise... trjconv to break the .trr into chunks, and now you can even do the analysis in parallel. 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] 2nd CMM 'Users Meet Developers' Workshop on QM/MM Simulations
Dear Colleague. We cordially invite you to register for attending the: 2nd CMM 'Users Meet Developers' Workshop on QM/MM Simulations August 24th to 26th in Philadelphia, PA * Goals The primary goals of this workshop are to encourage communication between different QM/MM approaches and implementations, exchange ideas about solutions to common problems and to discuss ways to make QM/MM calculations more accessible for newcomers to the field. To this effect, we would like to bring together active QM/MM code developers and experienced users. * Format The workshop will consist of selected presentations on current methods and applications of QM/MM simulations. The schedule will give a lot of room for discussions. We will start on Friday, August 24th in the 'early' morning (8.30am) and close on Sunday, August 26th around noon. Please note, that those are the 3 days directly after the 2007 Summer ACS meeting in Boston (which closes on Thursday). * Pre-Registration and Participation The workshop will be sponsored by the LRSM http://www.lrsm.upenn.edu through which we can provide accommodation in the form of a block of pre-reserved (double occupation) hotel rooms in a hotel that is a nice 20min walk (or a 5min bus ride) from the Penn campus and the lecture hall. The maximum number of participants and presenters, however, is limited due to limited funding, the size of the lecture hall, and to maintain the informal atmosphere which leaves much room for fruitful discussions. Interested parties can contact [EMAIL PROTECTED] stating their interest to participate, their background, affiliation and existing experience and - if applicable - suggesting a tentative title for a presentation. In order to bring in as many people as possible, we also kindly ask you to indicate whether you would be able to find (and/or fund) accommodation on your own. If notified in advance we can negotiate a discounted rate at the conference hotel. * Venue and Program The workshop will be held in the Carolyn Hoff Lynch Lecture Hall in the Cret wing of the Penn chemistry complex. The web page for the workshop is at http://www.cmm.upenn.edu/qmmm2007.html and currently still contains the details for last year's workshop (for your information). The web page will be updated as new information for this year's event becomes available. * Deadline Please respond to [EMAIL PROTECTED] until: May 12th 2007 Confirmation of your attendance will be sent out shortly after that date. We are hoping to meet you soon in Philadelphia. On behalf of the CMM and the organizers, Axel Kohlmeyer. ___ 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] do_dssp crashes on certain machines..
hi, On Thursday, 19. April 2007 17:23, Mark Abraham wrote: [EMAIL PROTECTED] wrote: Dear community, I have the following problem with do_dssp, when I try analysing a long 70 ns trajectory produced by a REMD calculation. All my previous analysis went fine, when the trajectory had a length of ~= 50ns. However, I now obtain the following errror message, perhaps one hour after launching do_dssp, when the standard error message says frames around 54ns are being analysed: Group12 ( Cl) has 8 elements Group13 ( SOL) has 42228 elements Group14 ( Other) has 42236 elements Select a group: There are 103 residues in your selected group Opening library file /home/coutinho/software/gromacs-3.3.0/icc9.0/share/gromacs/top/ss.map Reading frame 0 time0.000 Back Off! I just backed up ddKGQneH to ./#ddKGQneH.1# Reading frame 36630 time 54945.000 --- Program do_dssp, VERSION 3.3 Source code file: futil.c, line: 340 File input/output error: ddr3C7fs --- I guess this problem is due to the architecture/memory of the nodes of the cluster I use (where this error occurs whether do_dssp is the only job on the node or not): The same analysis works fine on another machine. The cluster I use is made of Hewlett-Packard ProLiant DL145 G2 AMD Opteron Model 246 nodes. The nodes contain two AMD opteron 2.4GHz cpus and 4*1GB memory. I thank you very much for any suggestions! Do the analysis piecewise... trjconv to break the .trr into chunks, and now you can even do the analysis in parallel. Could be a nice application for pushing parallel filesystems to its limits! Perhaps it could be implemented in upcoming gromacs versions, something like mpich wrapper for certain analysis tools. 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 Grettings, Florian -- --- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de --- ___ 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] 2nd CMM 'Users Meet Developers' Workshop on QM/MM Simulations
That is very interesting. I once did QM/MM with Gaussian and am thinking of using gromacs. How can I register? Thanks, --- Robert Johnson [EMAIL PROTECTED] wrote: Dear Colleague. We cordially invite you to register for attending the: 2nd CMM 'Users Meet Developers' Workshop on QM/MM Simulations August 24th to 26th in Philadelphia, PA * Goals The primary goals of this workshop are to encourage communication between different QM/MM approaches and implementations, exchange ideas about solutions to common problems and to discuss ways to make QM/MM calculations more accessible for newcomers to the field. To this effect, we would like to bring together active QM/MM code developers and experienced users. * Format The workshop will consist of selected presentations on current methods and applications of QM/MM simulations. The schedule will give a lot of room for discussions. We will start on Friday, August 24th in the 'early' morning (8.30am) and close on Sunday, August 26th around noon. Please note, that those are the 3 days directly after the 2007 Summer ACS meeting in Boston (which closes on Thursday). * Pre-Registration and Participation The workshop will be sponsored by the LRSM http://www.lrsm.upenn.edu through which we can provide accommodation in the form of a block of pre-reserved (double occupation) hotel rooms in a hotel that is a nice 20min walk (or a 5min bus ride) from the Penn campus and the lecture hall. The maximum number of participants and presenters, however, is limited due to limited funding, the size of the lecture hall, and to maintain the informal atmosphere which leaves much room for fruitful discussions. Interested parties can contact [EMAIL PROTECTED] stating their interest to participate, their background, affiliation and existing experience and - if applicable - suggesting a tentative title for a presentation. In order to bring in as many people as possible, we also kindly ask you to indicate whether you would be able to find (and/or fund) accommodation on your own. If notified in advance we can negotiate a discounted rate at the conference hotel. * Venue and Program The workshop will be held in the Carolyn Hoff Lynch Lecture Hall in the Cret wing of the Penn chemistry complex. The web page for the workshop is at http://www.cmm.upenn.edu/qmmm2007.html and currently still contains the details for last year's workshop (for your information). The web page will be updated as new information for this year's event becomes available. * Deadline Please respond to [EMAIL PROTECTED] until: May 12th 2007 Confirmation of your attendance will be sent out shortly after that date. We are hoping to meet you soon in Philadelphia. On behalf of the CMM and the organizers, Axel Kohlmeyer. ___ 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 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ 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] 2nd CMM 'Users Meet Developers' Workshop on QM/MM Simulations
Send an email to [EMAIL PROTECTED] On 4/19/07, yuemin liu [EMAIL PROTECTED] wrote: That is very interesting. I once did QM/MM with Gaussian and am thinking of using gromacs. How can I register? Thanks, --- Robert Johnson [EMAIL PROTECTED] wrote: Dear Colleague. We cordially invite you to register for attending the: 2nd CMM 'Users Meet Developers' Workshop on QM/MM Simulations August 24th to 26th in Philadelphia, PA * Goals The primary goals of this workshop are to encourage communication between different QM/MM approaches and implementations, exchange ideas about solutions to common problems and to discuss ways to make QM/MM calculations more accessible for newcomers to the field. To this effect, we would like to bring together active QM/MM code developers and experienced users. * Format The workshop will consist of selected presentations on current methods and applications of QM/MM simulations. The schedule will give a lot of room for discussions. We will start on Friday, August 24th in the 'early' morning (8.30am) and close on Sunday, August 26th around noon. Please note, that those are the 3 days directly after the 2007 Summer ACS meeting in Boston (which closes on Thursday). * Pre-Registration and Participation The workshop will be sponsored by the LRSM http://www.lrsm.upenn.edu through which we can provide accommodation in the form of a block of pre-reserved (double occupation) hotel rooms in a hotel that is a nice 20min walk (or a 5min bus ride) from the Penn campus and the lecture hall. The maximum number of participants and presenters, however, is limited due to limited funding, the size of the lecture hall, and to maintain the informal atmosphere which leaves much room for fruitful discussions. Interested parties can contact [EMAIL PROTECTED] stating their interest to participate, their background, affiliation and existing experience and - if applicable - suggesting a tentative title for a presentation. In order to bring in as many people as possible, we also kindly ask you to indicate whether you would be able to find (and/or fund) accommodation on your own. If notified in advance we can negotiate a discounted rate at the conference hotel. * Venue and Program The workshop will be held in the Carolyn Hoff Lynch Lecture Hall in the Cret wing of the Penn chemistry complex. The web page for the workshop is at http://www.cmm.upenn.edu/qmmm2007.html and currently still contains the details for last year's workshop (for your information). The web page will be updated as new information for this year's event becomes available. * Deadline Please respond to [EMAIL PROTECTED] until: May 12th 2007 Confirmation of your attendance will be sent out shortly after that date. We are hoping to meet you soon in Philadelphia. On behalf of the CMM and the organizers, Axel Kohlmeyer. ___ 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 __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ 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] soft-core potential in combination with PME
Hi, Tanks for your elaboration on the subject. I've done a couple of free energy simulations myself, also on disappearing charged atoms, but so far I've not yet encountered any of the instability problems you mention here (though I did encounter instabilities at high lamda values, caused by the flying ice cube problem). Your problem could very well be related to the force field, since I'm using G53a6 and you're probably using OPLS. Maybe the extra hydrogens are causing your troubles? I recommend Langevin dynamics (sd) to avoid the flying ice cube and related nonergodicity problems. I'm using AMBER. Yes, there are extra hydrogens. Related? Not sure. I agree with you that the ideal soft-core parameters for decoupling LJ may not be so ideal for decoupling Coulomb, and that this can lead to convergence problems and wrong free energy results. In that case a separate decoupling of LJ and Coulomb forces in fact may be the best answer. Right. Btw, David, are you still interested in feedback on your free energy tutorial, or do you consider that project finished? I used it as a starting point for my simulations and may have some interesting remarks and/or suggestions. It's not done; I need to do a much more extensive one at some point. I just put it up as a crude starting point. But feel free to send me comments off list if you have anything to say in terms of clarifications of the current one: I will be expanding it eventually, but in the meantime I can fix errors in the existing one or clarify. David Greetings, Jeroen Date: Fri, 13 Apr 2007 09:18:21 -0700 From: David Mobley [EMAIL PROTECTED] Subject: Re: [gmx-users] soft-core potential in combination with PME (sorry, again) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Berk and all, I don't understand what David Mobley meant exactly. There is no Coulomb singularity with soft-core. Maybe one could have an unfortunate situation where the LJ is already very soft, but the Coulomb not very soft, which could lead to instabilities. But I have never encountered this. Anytime I do a simulation where I turn of both coulomb and LJ interactions at the same time, I run into this problem. Sometimes it's worse than others. Maybe it's because the 1/r^12 and 1/r have different r-dependencies? I don't know. I suspect the issue partly is just what's optimal: The soft core parameters that would be optimal for modifying Coulomb interactions are not optimal for modifying LJ interactions, and vise versa. So if you use soft core settings that give you a smooth transformation for LJ interactions, you do too much or too little smoothing of the Coulomb interactions and introduce large Coulombic forces. On the other hand, if you pick soft core parameters that are good for Coulomb interactions, you end up with large LJ forces. (For example, Coulomb transformations are nearly optimal with LINEAR lambda scaling (sc-alpha=0), but that doesn't work *at all* for LJ transformations. If I remember correctly, basically what the Anwar paper tries to achieve is separately smoothing the two. You could probably accomplish the same thing by allowing separate sc-alpha and sc-power for Coulomb and LJ interactions so they can be tuned separately. So, while formally using soft core for Coulomb removes the singularity, in practice I think the forces are still large enough (when using soft core parameters are tuned for LJ interactions) that instabilities result (at least for the stuff I do, with the force field I use). Hence my recommendation to do two stages. Anecdotally, I should mention that a bunch of different people have e-mailed asking me about various problems they're having where they get unexpected free energies, etc. I suggest they do the Coulombic and LJ parts separately, and invariably they write back that it works much better. David ___ 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] Location of files under Cygwin
On 18 Apr 2007, Mark Abraham wrote: toma0052 wrote: Hello, I am looking to edit a little bit of the source code in Gromacs, and I am having a little bit of a problem. Normally, I am using Gromacs that is installed on a network, but I cannot edit this, so I also have Gromacs installed on a personal windows machine running Cygwin. The installation seemed to work fine, as I have run many md simulations, but my question is where are the mdlib files located? On the network Gromacs, the files are located in /usr/src/GROMACS/GCC/src/mdlib. But, under Cygwin, the folder /usr/src is empty. Am I missing something? Are the files located in another location? Did I need to include specific flags during the installation in order to have the source files in src/mdlib? Sorry if this is a silly question, but in searching the computer for update.c, I am coming up empty. Source files aren't installed anywhere by default, they get left where they are. Thus it seems your installation directory was cleaned away, if your search was complete. Thank you for the response. That seems to be the case. If I were to re-install Gromacs again, what should I do so that the installation directory and hence source files are not cleaned away? Last time I followed the instructions from the post: [gmx-users] HOWTO for installing non-MPI gromacs-3.3.1 on cygwin. What additional would I need to do to keep the source files? Thank you, Mike 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 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
[gmx-users] OPLS-AA dihedral angles
Hi all, I am trying to obtain proper dihedral parameters for CA-CT-CT-CA type, which is not in the OPLS-AA database. I have found a set for periodic dihedral type (from AMBER database) but I dont know how to convert that into RB form. GMX Manual does not mention how to convert periodic proper terms into RB form. So, my questions are:1) Can I put periodic dihedral parameters into OPLS-AA database?2) If (1) is no, then how can I convert periodic type into RB form? Is there any specific point to consider when using AMBER terms? (e.g. multiplying coefficients by 2) 3) Does anyone readily have the CA-CT-CT-CA dihedral parameters :) Thanks in advance,Murat CETINKAYA The Pennsylvania State University ___ 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] Failed Energy Minimization
Greetings:
I have been having trouble running any energy minimization with any
sort of system. I have small polypeptides in water, and then large
proteins in water with the same error message:
Steepest Descents:
Tolerance (Fmax) = 2.0e+02
Number of steps=1
Step=0, Dmax= 2.0e-02 nm, Epot= -2.84070e+04 Fmax= inf,
atom= 17
---
Program mdrun_d, VERSION 3.3.1
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or
parameter
errors that give particles very high velocities you might end up with
some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the
potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 ..
125 ]
Please report this to the mailing list (gmx-users@gromacs.org)
---
No matter what run parameters I get, I always get ci = -2147483648.
Even different systems. (This, I realize is simply numerically
infinity). If I try running with ns_type = simple, the em runs until it
hits around 35 and then says it didn't converge. Since I am running
grompp_d -v, I get that there are certain atoms that have infinite
potential. But, depending on the system, the atom type (solvent or
molecule) changes.
I have noted that previous posts have been answered with an admonition:
Find out which atoms are infinite force, and then fix it. I suppose I
could go through, find the atoms and remove those waters that overlap,
but shouldn't this be taken into account by the genbox_d program? I
also have tried to increase the vdw radii in the vdwradii.dat file to
have it delete more waters. But, even after having 60 fewer waters
around a 88 kD protein, the system still fails to energy minimize.
Given that this seems to be a common problem in solvating a system, are
there better options (options for genbox??) than running the following
shell commands? The em.mdp file is also shown below.
Thanks for your help,
Justin
# Set up the files
# First, the pdb is generated into a gro file, and other files
pdb2gmx_d -f ${INPUTPDB} -o ${MOL}.gro -i posre.itp -p ${MOL}_spc.top
-ter p2g.in
# Now modify the .pdb to use a periodic box
editconf_d -bt cubic -f ${MOL}.gro -o ${MOL}.gro -c -d ${PBCx}
#Solvate the box with spc, but the water type can be changed in next
line
genbox_d -cp ${MOL}.gro -cs spc216.gro -o ${MOL}-sol_b4em.gro -p
${MOL}_spc.top
# Now we specify which topology to use for our water (by default, SPC)
sed -e ${WATER} ${MOL}_spc.top ${MOL}-sol.top
# Now everything is solvated, so we switch molecular names (for
simplicity)
MOL=${MOL}-sol
# Perform Energy Minimization (necessary when solvating)
# GROmacs Pre-Processor
grompp_d -v -f em.mdp -c ${MOL}_b4em.gro -p ${MOL}.top -o ${MOL}_em
mdrun_d -v -s ${MOL}_em -o ${MOL}_em -c ${MOL}_b4eq
# Perform equilibration of the system
grompp_d -f eq.mdp -c ${MOL}_b4eq.gro -p ${MOL}.top -o ${MOL}_eq
mdrun_d -s ${MOL}_eq -o ${MOL}_eq -c ${MOL}_b4md
# Perform MD
grompp_d -f md.mdp -c ${MOL}_b4md.gro -p ${MOL}-v.top -o ${MOL}_md
mdrun_d -s ${MOL}_md -o ${MOL}_md -c ${MOL}_final
CUT=1.20
#--- Energy Minimization: em.mdp ---#
cat em.mdp EOF
title = ${MOL}
cpp = /usr/bin/cpp
define = -DFLEX
constraints = none
integrator = steep
nstlog = 100
ns_type = grid
dt = 0.001; ps !
nsteps = 1
nstlist = 1
coulombtype = PME
rlist = ${CUT}
rcoulomb= ${CUT}
rvdw= ${CUT}
pme_order = 6
fourierspacing = 0.05
ewald_rtol = 1e-5
;
; Energy minimizing stuff
;
emstep = 0.02
emtol = 200.0
EOF
_
Justin M. Shorb Phone: (608) 262-0483
Skinner Group [EMAIL PROTECTED]
University of Wisconsin-Madison, Department of Chemistry
1101 University Ave., Madison, WI, 53706
___
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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
Re: [gmx-users] Location of files under Cygwin
toma0052 wrote: Source files aren't installed anywhere by default, they get left where they are. Thus it seems your installation directory was cleaned away, if your search was complete. Thank you for the response. That seems to be the case. If I were to re-install Gromacs again, what should I do so that the installation directory and hence source files are not cleaned away? Last time I followed the instructions from the post: [gmx-users] HOWTO for installing non-MPI gromacs-3.3.1 on cygwin. What additional would I need to do to keep the source files? You'd need to not clean them away. That HOWTO I wrote is silent about what to do with your installation directory that includes the source. You may as well leave it (having possibly done make clean to get rid of useless object files, unless you're planning rebuilds). Or you can unpack the source again and put it anywhere that strikes your fancy. There's not many rules for Cygwin, especially not for things that don't have to interact with anything else, such as a passive source distribution. 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
Re: [gmx-users] OPLS-AA dihedral angles
MURAT CETINKAYA wrote: Hi all, I am trying to obtain proper dihedral parameters for CA-CT-CT-CA type, which is not in the OPLS-AA database. I have found a set for periodic dihedral type (from AMBER database) but I dont know how to convert that into RB form. GMX Manual does not mention how to convert periodic proper terms into RB form. Mixing and matching parameters from different forcefields is usually a bad idea. Force fields are artificial constructs optimized to reproduce some subset of experimental and computational results. There's no reason for the CA-CA-CA-CA dihedrals to resemble each other in different force fields, and thus no reason for them to interact sanely with the rest of each other's force fields. Can you use a whole AMBER force field? So, my questions are: 1) Can I put periodic dihedral parameters into OPLS-AA database? Yup. Get out your trigonometry - for values of periodicity below 6, you can convert periodic to RB forms, but read the relevant sections of chapter 4 and 5 of the GROMACS manuals (and the AMBER documentation!) to get sign conventions right. 2) If (1) is no, then how can I convert periodic type into RB form? Is there any specific point to consider when using AMBER terms? (e.g. multiplying coefficients by 2) 3) Does anyone readily have the CA-CT-CT-CA dihedral parameters :) Not I. 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
Re: [gmx-users] Failed Energy Minimization
Justin M. Shorb wrote: Greetings: I have been having trouble running any energy minimization with any sort of system. I have small polypeptides in water, and then large proteins in water with the same error message: No matter what run parameters I get, I always get ci = -2147483648. Even different systems. (This, I realize is simply numerically infinity). If I try running with ns_type = simple, the em runs until it hits around 35 and then says it didn't converge. Since I am running grompp_d -v, I get that there are certain atoms that have infinite potential. But, depending on the system, the atom type (solvent or molecule) changes. This suggests a problem with your force field and/or topology. I have noted that previous posts have been answered with an admonition: Find out which atoms are infinite force, and then fix it. I suppose I could go through, find the atoms and remove those waters that overlap, but shouldn't this be taken into account by the genbox_d program? I also have tried to increase the vdw radii in the vdwradii.dat file to have it delete more waters. But, even after having 60 fewer waters around a 88 kD protein, the system still fails to energy minimize. This suggests that the source of the problem isn't that these atoms start life too close together, but maybe they're moving too close together because of some other problem? (Unless the error is always happening before the first EM step) Given that this seems to be a common problem in solvating a system, are there better options (options for genbox??) than running the following shell commands? The em.mdp file is also shown below. That all seems fine. 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
