Re: [gmx-users] Solvent molecules within a certain distance of solute
g_hbond and g_hbond -contact Erik On 22 May 2013, at 05:37, Vishal Kumar Jaiswal vishal3...@gmail.com wrote: Hello gromacs users I performed a 1 ns simulation of N-isopropylamide in water. Now i wish to calculate the average no of water molecules(averaged over entire trajectory) within a certain distance of solute and no. of water molecules that form H-bonds with solute. Could you guide me as to what tools are appropriate for this Vishal Undergraduate student IITG -- 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 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] parameter files for cholesteryl ester
Dear all, I want to simulate a system consisting of cholesteryl ester. I have to use charmm27 all atom force field for which I am not able to get the parameters. I tried using lipid book but did not find any files. As I am a new beginner to performing simulations, I have no idea about other sources from where I could get the parameter files. Kindly provide your valuable suggestions. Thanks in advance. Revthi -- 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] MSD and frequency of writing trajectories
Dear Gromacs Users, I have a question interpreting obtained msd data. I need to calculate diffusion coefficient for a single argon atom in a box of water (500 molecules). During the calculations (50ns) I write both trr and xtc trajectories, but to save space I write trr for whole system very seldom (every 5 steps = 100 ps) but in xtc I have argon only (no water) and write more often (every 1000 steps = 2 ps). When I analysed the results using g_msd I was surprised that the msd curves obtained from trr and xtc trajectories differ a lot, what affect the resulting diffusion coefficients. If I save trr more often, like every 1 steps (20ps) the results from both files coincide. Does the msd results depend on how often you write trajectories? If yes, what frequency for writing the trajectories for future calculation of the diffusion coefficient would be reasonable and how long should be the calculations? Thanks you Anna --- Dr Anna Akinshina School of Chemical Engineering Analytical Science The University of Manchester, UK -- 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] error in running g_dist
Respected sir I want to calculate the distance between protein and ligand after I have run the production step. I used the following command.. g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx Groups I selected was Group 1 (protein) Group 13 (ligand) It says the following error Molecule in topology has atom numbers below and above natoms (11793). You are probably trying to use a trajectory which does not match the first 11793 atoms of the run input file. how to debug the error... -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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] Free energy of solvation's .mdp of peptide
Hi, if I want to calculate the free energy of solvation of peptide, because both van der Waals and Coulombic interactions are important for peptide so I set couple-lambda0 = none couple-lambda1 = vdw-q is it right? or it's better to choose wo-stage approach to do this work: van der Waals coupling: sc-alpha = 0.5 ; use soft-core for LJ (de)coupling sc-sigma = 0.3 sc-power = 1 couple-moltype= peptide couple-intramol = no couple-lambda0= none; non-interacting dummy in state A couple-lambda1= vdw ; only vdW terms on in state B Coulombic coupling: sc-alpha = 0 ; soft-core during (dis)charging can be unstable! sc-sigma = 0 couple-moltype= peptide couple-intramol = no couple-lambda0= vdw ; only vdW terms in state A (the previous state B is now A) couple-lambda1= vdw-q ; all nonbonded interactions are on in state B Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Free-energy-of-solvation-s-mdp-of-peptide-tp5008445.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] MSD and frequency of writing trajectories
Hi, For particles that diffuse more than half a box length between frames will appear as if they haven't moved much, assuming you have periodic boundary conditions. Erik On 22 May 2013, at 11:41, Anna Akinshina anna.akinsh...@manchester.ac.uk wrote: Dear Gromacs Users, I have a question interpreting obtained msd data. I need to calculate diffusion coefficient for a single argon atom in a box of water (500 molecules). During the calculations (50ns) I write both trr and xtc trajectories, but to save space I write trr for whole system very seldom (every 5 steps = 100 ps) but in xtc I have argon only (no water) and write more often (every 1000 steps = 2 ps). When I analysed the results using g_msd I was surprised that the msd curves obtained from trr and xtc trajectories differ a lot, what affect the resulting diffusion coefficients. If I save trr more often, like every 1 steps (20ps) the results from both files coincide. Does the msd results depend on how often you write trajectories? If yes, what frequency for writing the trajectories for future calculation of the diffusion coefficient would be reasonable and how long should be the calculations? Thanks you Anna --- Dr Anna Akinshina School of Chemical Engineering Analytical Science The University of Manchester, UK -- 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 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] MSD and frequency of writing trajectories
Sure. What's the MSD of a pendulum if you only sample at a rate equal to the period? How often you want to sample depends on the time scale of what you want to observe. That might be up to you to measure :-) Mark On Wed, May 22, 2013 at 11:41 AM, Anna Akinshina anna.akinsh...@manchester.ac.uk wrote: Dear Gromacs Users, I have a question interpreting obtained msd data. I need to calculate diffusion coefficient for a single argon atom in a box of water (500 molecules). During the calculations (50ns) I write both trr and xtc trajectories, but to save space I write trr for whole system very seldom (every 5 steps = 100 ps) but in xtc I have argon only (no water) and write more often (every 1000 steps = 2 ps). When I analysed the results using g_msd I was surprised that the msd curves obtained from trr and xtc trajectories differ a lot, what affect the resulting diffusion coefficients. If I save trr more often, like every 1 steps (20ps) the results from both files coincide. Does the msd results depend on how often you write trajectories? If yes, what frequency for writing the trajectories for future calculation of the diffusion coefficient would be reasonable and how long should be the calculations? Thanks you Anna --- Dr Anna Akinshina School of Chemical Engineering Analytical Science The University of Manchester, UK -- 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 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] error in running g_dist
Use gmxcheck to find out what's in the files. Think about how you used xtcgroups. Consider using tpbconv to make a matching subset from your .tpr. Mark On Wed, May 22, 2013 at 11:53 AM, Arunima Shilpi writetoas...@gmail.comwrote: Respected sir I want to calculate the distance between protein and ligand after I have run the production step. I used the following command.. g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx Groups I selected was Group 1 (protein) Group 13 (ligand) It says the following error Molecule in topology has atom numbers below and above natoms (11793). You are probably trying to use a trajectory which does not match the first 11793 atoms of the run input file. how to debug the error... -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 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] C6 C12 parameters for non-bonded interactions using tables
Greetings, I am trying to use tabulated potentials for the VdW interactions between TIP5P water molecules. I have tested my topology file to make sure that it gives reasonable results with the standard table6-12.xvg in the /top folder and C6=4*eps*sig^6 , C12=4*eps*sig^12. I am able to match the energies with an identical run not using look-up tables. The problem comes when I want to include the C6 C12 parameters within the table. This is needed for dealing with more complex multi-parameter potential functions. I tried testing this with the standard Lennard-Jones potential. Setting g(r)=-(4*eps*sig^6)/r^6 and h(r)=(4*eps*sig^12)/r^12. I then construct my table according to [r,f(r),-f'(r),g(r),-g'(r),h(r),-h'(r)] I set vdw-type = user in my mdp file and modified my topology so that: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 yes 0.5 0.8333 [ atomtypes ] ; name at.num mass charge ptype C6 C12 OW_tip5p 8 16.000. A 1.0e+00 1.0e+00 Since C6 C12 = 1, this run should be identical to using the table6-12.xvg and C6=4*eps*sig^6 , C12=4*eps*sig^12 The run proceeds fine with no warnings or errors, but the LJ and Potential energies are an order of magnitude higher than when using the standard table. I don't understand why I am not able to reproduce the results by this method? Thanks, Andrish -- View this message in context: http://gromacs.5086.x6.nabble.com/C6-C12-parameters-for-non-bonded-interactions-using-tables-tp5008449.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: error in running g_dist
Arunima Shilpi-2 wrote Respected sir I want to calculate the distance between protein and ligand after I have run the production step. I used the following command.. g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx Groups I selected was Group 1 (protein) Group 13 (ligand) It says the following error Molecule in topology has atom numbers below and above natoms (11793). You are probably trying to use a trajectory which does not match the first 11793 atoms of the run input file. how to debug the error... -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- gmx-users mailing list gmx-users@ 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-request@ . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Did you check that this You are probably trying to use a trajectory which does not match the first 11793 atoms of the run input file. is not the case? Andrish -- View this message in context: http://gromacs.5086.x6.nabble.com/error-in-running-g-dist-tp5008444p5008450.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] C6 C12 parameters for non-bonded interactions using tables
Exactly a factor of ten? Angstrom vs nm issue? On Wed, May 22, 2013 at 4:09 PM, Andrish Reddy are...@csir.co.za wrote: Greetings, I am trying to use tabulated potentials for the VdW interactions between TIP5P water molecules. I have tested my topology file to make sure that it gives reasonable results with the standard table6-12.xvg in the /top folder and C6=4*eps*sig^6 , C12=4*eps*sig^12. I am able to match the energies with an identical run not using look-up tables. The problem comes when I want to include the C6 C12 parameters within the table. This is needed for dealing with more complex multi-parameter potential functions. I tried testing this with the standard Lennard-Jones potential. Setting g(r)=-(4*eps*sig^6)/r^6 and h(r)=(4*eps*sig^12)/r^12. I then construct my table according to [r,f(r),-f'(r),g(r),-g'(r),h(r),-h'(r)] I set vdw-type = user in my mdp file and modified my topology so that: [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 yes 0.5 0.8333 [ atomtypes ] ; name at.num mass charge ptype C6 C12 OW_tip5p 8 16.000. A 1.0e+00 1.0e+00 Since C6 C12 = 1, this run should be identical to using the table6-12.xvg and C6=4*eps*sig^6 , C12=4*eps*sig^12 The run proceeds fine with no warnings or errors, but the LJ and Potential energies are an order of magnitude higher than when using the standard table. I don't understand why I am not able to reproduce the results by this method? Thanks, Andrish -- View this message in context: http://gromacs.5086.x6.nabble.com/C6-C12-parameters-for-non-bonded-interactions-using-tables-tp5008449.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 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] COM coordinate fix
Dear all, We have 80 polymers in the simulation box, for some reason, we want to make the COM of each polymer be fixed. Is this possible in Gromacs with any command, or somewhere in the source code we can change the expression of displacement along with time . Thank you very much in advance. Kind regards, Li -- 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] Velocity autocorrelation problem
Dear all, I am trying to use g_velacc to calculate diffusion coefficient for a single polymer chain. As I follow the Gromacs tutorial and use the command (version 4.5.1) g_velacc -acflen 1001 -nonormalize -mol -n atoms.ndx -s topol.tpr the ACF is always zero. However, if I remove -mol option, the data shows up. It looks like -mol is a default option for the calculation so I don't know if it is still necessary to add it, or is it just a bug in the program? Thank you! Shirley On May 22, 2013, at 10:31 AM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Free energy of solvation's .mdp of peptide (maggin) 2. Re: MSD and frequency of writing trajectories (Erik Marklund) 3. Re: MSD and frequency of writing trajectories (Mark Abraham) 4. Re: error in running g_dist (Mark Abraham) 5. C6 C12 parameters for non-bonded interactions usingtables (Andrish Reddy) 6. Re: error in running g_dist (Andrish Reddy) 7. Re: C6 C12 parameters for non-bonded interactions using tables (Mark Abraham) 8. COM coordinate fix (l@utwente.nl) -- Message: 1 Date: Wed, 22 May 2013 04:14:31 -0700 (PDT) From: maggin maggin.c...@gmail.com Subject: [gmx-users] Free energy of solvation's .mdp of peptide To: gmx-users@gromacs.org Message-ID: 1369221271481-5008445.p...@n6.nabble.com Content-Type: text/plain; charset=us-ascii Hi, if I want to calculate the free energy of solvation of peptide, because both van der Waals and Coulombic interactions are important for peptide so I set couple-lambda0 = none couple-lambda1 = vdw-q is it right? or it's better to choose wo-stage approach to do this work: van der Waals coupling: sc-alpha = 0.5 ; use soft-core for LJ (de)coupling sc-sigma = 0.3 sc-power = 1 couple-moltype= peptide couple-intramol = no couple-lambda0= none; non-interacting dummy in state A couple-lambda1= vdw ; only vdW terms on in state B Coulombic coupling: sc-alpha = 0 ; soft-core during (dis)charging can be unstable! sc-sigma = 0 couple-moltype= peptide couple-intramol = no couple-lambda0= vdw ; only vdW terms in state A (the previous state B is now A) couple-lambda1= vdw-q ; all nonbonded interactions are on in state B Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/Free-energy-of-solvation-s-mdp-of-peptide-tp5008445.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Message: 2 Date: Wed, 22 May 2013 13:17:41 +0200 From: Erik Marklund er...@xray.bmc.uu.se Subject: Re: [gmx-users] MSD and frequency of writing trajectories To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 1efe1d47-497a-44fc-99b2-a8210d2c0...@xray.bmc.uu.se Content-Type: text/plain; charset=us-ascii Hi, For particles that diffuse more than half a box length between frames will appear as if they haven't moved much, assuming you have periodic boundary conditions. Erik On 22 May 2013, at 11:41, Anna Akinshina anna.akinsh...@manchester.ac.uk wrote: Dear Gromacs Users, I have a question interpreting obtained msd data. I need to calculate diffusion coefficient for a single argon atom in a box of water (500 molecules). During the calculations (50ns) I write both trr and xtc trajectories, but to save space I write trr for whole system very seldom (every 5 steps = 100 ps) but in xtc I have argon only (no water) and write more often (every 1000 steps = 2 ps). When I analysed the results using g_msd I was surprised that the msd curves obtained from trr and xtc trajectories differ a lot, what affect the resulting diffusion coefficients. If I save trr more often, like every 1 steps (20ps) the results from both files coincide. Does the msd results depend on how often you write trajectories? If yes, what frequency for writing the trajectories for future calculation of the diffusion coefficient would be reasonable and how long should be the calculations? Thanks you Anna --- Dr Anna Akinshina School of Chemical Engineering Analytical Science The University of Manchester, UK -- gmx-users mailing list
[gmx-users] Re: MSD and frequency of writing trajectories
Erik, Do you mean that if the particle diffuses too fast, it will appear like it doesn't move because of the PBC? I have another issue. If I have a polymer chain with the length almost the same as the box length. It is possible that the COM diffusion of the chain may appear it does not move or move backward due to PBC, right? Thank you so much! Shirley On May 22, 2013, at 10:31 AM, gmx-users-requ...@gromacs.org wrote: Re: MSD and frequency of writing trajectories -- 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
Aw: [gmx-users] C6 C12 parameters for non-bonded interactions using tables
Dear Andrish Reddy, Dont know if it works but I have for small molecules just put all the parmeters within the .top file right below the defaults, instead of user defined tables, and removed the forcefieldX/SPC.itp or equivalent section so it doesnt loop, but dont know if it works in your case. Just a quick suggestion to try, as I parse e-mails. Smone else probably has better answeres though... Stephan Gesendet:Mittwoch, 22. Mai 2013 um 16:09 Uhr Von:Andrish Reddy are...@csir.co.za An:gmx-users@gromacs.org Betreff:[gmx-users] C6 C12 parameters for non-bonded interactions using tables Greetings, I am trying to use tabulated potentials for the VdW interactions between TIP5P water molecules. I have tested my topology file to make sure that it gives reasonable results with the standard table6-12.xvg in the /top folder and C6=4*eps*sig^6 , C12=4*eps*sig^12. I am able to match the energies with an identical run not using look-up tables. The problem comes when I want to include the C6 C12 parameters within the table. This is needed for dealing with more complex multi-parameter potential functions. I tried testing this with the standard Lennard-Jones potential. Setting g(r)=-(4*eps*sig^6)/r^6 and h(r)=(4*eps*sig^12)/r^12. I then construct my table according to [r,f(r),-f(r),g(r),-g(r),h(r),-h(r)] I set vdw-type = user in my mdp file and modified my topology so that: [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 1 yes 0.5 0.8333 [ atomtypes ] ; name at.num mass charge ptype C6 C12 OW_tip5p 8 16.00 0. A 1.0e+00 1.0e+00 Since C6 C12 = 1, this run should be identical to using the table6-12.xvg and C6=4*eps*sig^6 , C12=4*eps*sig^12 The run proceeds fine with no warnings or errors, but the LJ and Potential energies are an order of magnitude higher than when using the standard table. I dont understand why I am not able to reproduce the results by this method? Thanks, Andrish -- View this message in context: http://gromacs.5086.x6.nabble.com/C6-C12-parameters-for-non-bonded-interactions-using-tables-tp5008449.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Different Cutoff Options
Hi, I'm trying to understand how best to compare performance of Gromacs 4.6.1 on CPU only versus CPU plus GPU on a cluster. Each node has is 2 x 8 Core Sandy Bridge + 1 Nvidia M2090. I've been trying to use the d.dppc benchmark (with modifications). I would like to profile both standard cutoff and pme electrostatics on the CPU and GPU (as this is building on benchmarking work done on the CPU only which used these benchmarks). While I have successfully run modifications of the d.dppc benchmark utilising both the CPU and GPU I have some questions about the different options. As a beginner with MD and Gromacs could somebody elaborate on the table comparing Group and Verlet schemes on this page: http://www.gromacs.org/Documentation/Cut-off_schemes In particular the table shows which non-bonded interaction features are supported by both the group and verlet schemes. In the table we see four different 'cutoff' non-bonded interaction features listed: unbuffered cut-off scheme buffered cut-off scheme exact cut-off cut-off If plain 'cut-off' is not one of the three more specific schemes listed above it, how does it differ from each of them? The d.dppc input file as provided is: title= dppc cpp = /lib/cpp integrator = md nsteps = 5000 nstlist = 10 nstxout = 0 nstvout = 0 nstxtcout= 0 nstlog = 0 dt = 0.002 constraints = all-bonds nstenergy= 0 ns_type = grid coulombtype = cut-off rlist= 1.0 rvdw = 1.0 rcoulomb = 1.8 tcoupl = berendsen tc_grps = dppc sol tau_t= 0.1 0.1 ref_t= 323 323 Pcoupl = no Could you say which of the four cutoff types mentioned above these settings equate to and how these setting should be changed to equate to each of the other three cutoff types? -- View this message in context: http://gromacs.5086.x6.nabble.com/Different-Cutoff-Options-tp5008455.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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: Aw: [gmx-users] C6 C12 parameters for non-bonded interactions using tables
lloyd riggs wrote nbsp; Dear Andrish Reddy, nbsp; Dont know if it works but I have for small molecules just put all the parmeters within the .top file right below the defaults, instead of user defined tables, and removed the quot;forcefieldX/SPC.itpquot; or equivalent section so it doesn#39;t loop, but dont know if it works in your case.nbsp; Just a quick suggestion to try, as I parse e-mails.nbsp; Smone else probably has better answeres though... nbsp; Stephan Gesendet:nbsp;Mittwoch, 22. Mai 2013 um 16:09 Uhr Von:nbsp;quot;Andrish Reddyquot; lt; areddy@.co gt; An:nbsp; gmx-users@ Betreff:nbsp;[gmx-users] C6 amp; C12 parameters for non-bonded interactions using tables Greetings, I am trying to use tabulated potentials for the VdW interactions between TIP5P water molecules. I have tested my topology file to make sure that it gives reasonable results with the standard table6-12.xvg in the /top folder and C6=4*eps*sig^6 , C12=4*eps*sig^12. I am able to match the energies with an identical run not using look-up tables. The problem comes when I want to include the C6 amp; C12 parameters within the table. This is needed for dealing with more complex multi-parameter potential functions. I tried testing this with the standard Lennard-Jones potential. Setting g(r)=-(4*eps*sig^6)/r^6 and h(r)=(4*eps*sig^12)/r^12. I then construct my table according to [r,f(r),-f#39;(r),g(r),-g#39;(r),h(r),-h#39;(r)] I set vdw-type = user in my mdp file and modified my topology so that: [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 1 yes 0.5 0.8333 [ atomtypes ] ; name at.num mass charge ptype C6 C12 OW_tip5p 8 16.00 0. A 1.0e+00 1.0e+00 Since C6 amp; C12 = 1, this run should be identical to using the table6-12.xvg and C6=4*eps*sig^6 , C12=4*eps*sig^12 The run proceeds fine with no warnings or errors, but the LJ and Potential energies are an order of magnitude higher than when using the standard table. I don#39;t understand why I am not able to reproduce the results by this method? Thanks, Andrish -- View this message in context: http://gromacs.5086.x6.nabble.com/C6-C12-parameters-for-non-bonded-interactions-using-tables-tp5008449.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@ 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#39;t post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request@ . * Can#39;t post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@ 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-request@ . * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Thanks Stephan, Don't think that will work in my case. Andrish -- View this message in context: http://gromacs.5086.x6.nabble.com/C6-C12-parameters-for-non-bonded-interactions-using-tables-tp5008449p5008456.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Re: MSD and frequency of writing trajectories
On Wed, May 22, 2013 at 4:49 PM, Yutian Yang yyan...@syr.edu wrote: Erik, Do you mean that if the particle diffuses too fast, it will appear like it doesn't move because of the PBC? Sure. http://en.wikipedia.org/wiki/Stroboscopic_effect I have another issue. If I have a polymer chain with the length almost the same as the box length. It is possible that the COM diffusion of the chain may appear it does not move or move backward due to PBC, right? Depends how you've post-processed your trajectory and/or the GROMACS tool treats PBC. There have been bugs in the latter. Nobody's issued any warranties, so everyone should certainly be checking a) that the tool works they way they think it does, and b) that the tool gives the right answer on a relevant test case. Or the world may end when some reviewer points out an analysis artefact some dark day... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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] Re: MSD and frequency of writing trajectories
Hi Mark, Regarding your statement, how does one check whether g_msd has removed pbc correctly or not? Thanks On Wed, May 22, 2013 at 10:56 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Wed, May 22, 2013 at 4:49 PM, Yutian Yang yyan...@syr.edu wrote: Erik, Do you mean that if the particle diffuses too fast, it will appear like it doesn't move because of the PBC? Sure. http://en.wikipedia.org/wiki/Stroboscopic_effect I have another issue. If I have a polymer chain with the length almost the same as the box length. It is possible that the COM diffusion of the chain may appear it does not move or move backward due to PBC, right? Depends how you've post-processed your trajectory and/or the GROMACS tool treats PBC. There have been bugs in the latter. Nobody's issued any warranties, so everyone should certainly be checking a) that the tool works they way they think it does, and b) that the tool gives the right answer on a relevant test case. Or the world may end when some reviewer points out an analysis artefact some dark day... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Re: MSD and frequency of writing trajectories
Along the lines of take a trajectory, and look through it for a frame where it crosses the periodic boundary of the original cell. Look for artefacts in the analysis at that time. Or take that frame and use it as a reference state for whatever trjconv-based PBC-massaging workflow you previously used before your analysis. How best to test depends exactly what you're measuring. There are too many combinations in most GROMACS tools for one test to prove the whole tool works correctly (or even agrees with how you think it works), so you need to think about the context that matters to you. You can probably get creative with editconf's translation options and come up with some fake trajectories via trjcat that test some edge cases relevant to what you want to do. Mark On Wed, May 22, 2013 at 7:40 PM, rajat desikan rajatdesi...@gmail.comwrote: Hi Mark, Regarding your statement, how does one check whether g_msd has removed pbc correctly or not? Thanks On Wed, May 22, 2013 at 10:56 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, May 22, 2013 at 4:49 PM, Yutian Yang yyan...@syr.edu wrote: Erik, Do you mean that if the particle diffuses too fast, it will appear like it doesn't move because of the PBC? Sure. http://en.wikipedia.org/wiki/Stroboscopic_effect I have another issue. If I have a polymer chain with the length almost the same as the box length. It is possible that the COM diffusion of the chain may appear it does not move or move backward due to PBC, right? Depends how you've post-processed your trajectory and/or the GROMACS tool treats PBC. There have been bugs in the latter. Nobody's issued any warranties, so everyone should certainly be checking a) that the tool works they way they think it does, and b) that the tool gives the right answer on a relevant test case. Or the world may end when some reviewer points out an analysis artefact some dark day... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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 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] Re: MSD and frequency of writing trajectories
Thanks for the reply, trjconv does not have any bugs in removing pbc, right? We can just feed the -nojump output to g_msd. I am going to output the coordinates and velocities with g_traj and run it through my own code :) On Wed, May 22, 2013 at 11:19 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Along the lines of take a trajectory, and look through it for a frame where it crosses the periodic boundary of the original cell. Look for artefacts in the analysis at that time. Or take that frame and use it as a reference state for whatever trjconv-based PBC-massaging workflow you previously used before your analysis. How best to test depends exactly what you're measuring. There are too many combinations in most GROMACS tools for one test to prove the whole tool works correctly (or even agrees with how you think it works), so you need to think about the context that matters to you. You can probably get creative with editconf's translation options and come up with some fake trajectories via trjcat that test some edge cases relevant to what you want to do. Mark On Wed, May 22, 2013 at 7:40 PM, rajat desikan rajatdesi...@gmail.com wrote: Hi Mark, Regarding your statement, how does one check whether g_msd has removed pbc correctly or not? Thanks On Wed, May 22, 2013 at 10:56 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, May 22, 2013 at 4:49 PM, Yutian Yang yyan...@syr.edu wrote: Erik, Do you mean that if the particle diffuses too fast, it will appear like it doesn't move because of the PBC? Sure. http://en.wikipedia.org/wiki/Stroboscopic_effect I have another issue. If I have a polymer chain with the length almost the same as the box length. It is possible that the COM diffusion of the chain may appear it does not move or move backward due to PBC, right? Depends how you've post-processed your trajectory and/or the GROMACS tool treats PBC. There have been bugs in the latter. Nobody's issued any warranties, so everyone should certainly be checking a) that the tool works they way they think it does, and b) that the tool gives the right answer on a relevant test case. Or the world may end when some reviewer points out an analysis artefact some dark day... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Effect of pressure coupling frequency on gpu simulations
On Wed, May 22, 2013 at 6:32 AM, Trayder trayder.tho...@monash.edu wrote: Hi all, I've been running 5fs timestep simulations successfully without gpus (united-atom, HEAVYH). When continuing the same simulations on a gpu cluster utilising the verlet cutoff-scheme they crash within 20 steps. Reducing the timestep to 2fs runs smoothly, however I noticed the message: Making this change manually led to crashing simulations as nstcalclr, nsttcouple and nstpcouple default to the value of nstlist. After defining them all separately I was able to determine that the simulation exploding was dependent entirely on nstpcouple and by lowering it to 5 (from the default 10) I was able to run simulations at a 5fs timestep. So, my questions: Is lowering nstpcouple a legitimate solution or just a bandaid? P-R does not cope well with situations where the box size changes enough (e.g. you should normally avoid it during equilibration). nstpcouple != 1 means that you simulate on an NVE manifold for a period of time (maybe with some T changes if nsttcouple != nstpcouple), and I'd suppose the longer that interval the bigger the chance of a build-up of pressure that P-R will then try to relieve by changing the box size. Larger nstlist and dt will exacerbate this, of course. I would recommend you experiment and see how far you can push things and keep statistics that still resemble those with small nstpcouple. Larger nstpcouple helps reduce the frequency with which global communication occurs, and that affects your simulation rate... life is complex! It would be nice if we were able to compute heuristics so that mdrun could anticipate such a problem and warn you, but off-hand that seems a tricky problem... The simulation runs with nstcalclr and nsttcouple set to 50 along with nstcalclr should have no effect - it works only with the group scheme, which does not work on GPUs. nstlist. Is nstlist the only setting that should be increased when utilising gpus? Yes, AFAIK. The point is that nstlist is the interval between neighbour searches, and (at the moment at least) that's only done on the CPU. The Verlet kernels cheerfully compute lots of zero-strength interactions outside the cutoff (by design), and depending on the relative performance of your hardware it is normally more efficient to bump nstlist up (and rlist accordingly, to provide a larger buffer for diffusion of particles) and compute more zeroes than it is to search for neighbours more often. Mark Thanks in advance, -Trayder P.S. The working mdp file: -- View this message in context: http://gromacs.5086.x6.nabble.com/Effect-of-pressure-coupling-frequency-on-gpu-simulations-tp5008439.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 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] Re: MSD and frequency of writing trajectories
On Wed, May 22, 2013 at 8:05 PM, rajat desikan rajatdesi...@gmail.comwrote: Thanks for the reply, trjconv does not have any bugs in removing pbc, right? We can just feed the -nojump output to g_msd. Maybe. There are not (yet) any automated tests for the code in these tools. But probably trjconv -nojump works correctly else we'd have heard more screaming... Mark I am going to output the coordinates and velocities with g_traj and run it through my own code :) On Wed, May 22, 2013 at 11:19 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Along the lines of take a trajectory, and look through it for a frame where it crosses the periodic boundary of the original cell. Look for artefacts in the analysis at that time. Or take that frame and use it as a reference state for whatever trjconv-based PBC-massaging workflow you previously used before your analysis. How best to test depends exactly what you're measuring. There are too many combinations in most GROMACS tools for one test to prove the whole tool works correctly (or even agrees with how you think it works), so you need to think about the context that matters to you. You can probably get creative with editconf's translation options and come up with some fake trajectories via trjcat that test some edge cases relevant to what you want to do. Mark On Wed, May 22, 2013 at 7:40 PM, rajat desikan rajatdesi...@gmail.com wrote: Hi Mark, Regarding your statement, how does one check whether g_msd has removed pbc correctly or not? Thanks On Wed, May 22, 2013 at 10:56 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, May 22, 2013 at 4:49 PM, Yutian Yang yyan...@syr.edu wrote: Erik, Do you mean that if the particle diffuses too fast, it will appear like it doesn't move because of the PBC? Sure. http://en.wikipedia.org/wiki/Stroboscopic_effect I have another issue. If I have a polymer chain with the length almost the same as the box length. It is possible that the COM diffusion of the chain may appear it does not move or move backward due to PBC, right? Depends how you've post-processed your trajectory and/or the GROMACS tool treats PBC. There have been bugs in the latter. Nobody's issued any warranties, so everyone should certainly be checking a) that the tool works they way they think it does, and b) that the tool gives the right answer on a relevant test case. Or the world may end when some reviewer points out an analysis artefact some dark day... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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 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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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 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
[gmx-users] Re: REMD analysis
Dear Sir, I performed another round of trial with different set of temperature and I got the avg accp. ration around 0.22. Here's the temp. dist. that I used : 250 268 288 308 331 355 380 408 438 469 503 540 579 621 I then checked the replica_index and replica_temp files for each replica individually. The plots are exactly similar for all the replicas, as an eg. here's the link for first three replicas . https://www.dropbox.com/s/cuydj010wh2hgkt/replica_index0.pnghttps://www.dropbox.com/s/cuydj010wh2hgkt/replica_index0.png;cid=1368714426780-10 https://www.dropbox.com/s/q01wluh8wxlcxs8/replica_index1.pnghttps://www.dropbox.com/s/q01wluh8wxlcxs8/replica_index1.png;cid=1368714426780-10 https://www.dropbox.com/s/cm9f8qo1afo6w4k/replica_index2.pnghttps://www.dropbox.com/s/cm9f8qo1afo6w4k/replica_index2.png;cid=1368714426780-10 https://www.dropbox.com/s/gkbu0g0e1r37l57/replica_temp0.pnghttps://www.dropbox.com/s/gkbu0g0e1r37l57/replica_temp0.png;cid=1368714426780-10 https://www.dropbox.com/s/sffq8rwghjublu0/replica_temp1.pnghttps://www.dropbox.com/s/sffq8rwghjublu0/replica_temp1.png;cid=1368714426780-10 https://www.dropbox.com/s/ulccw8xabj66ktm/replica_temp2.pnghttps://www.dropbox.com/s/ulccw8xabj66ktm/replica_temp2.png;cid=1368714426780-10 I checked the PE overlap also, that looks fine ( https://www.dropbox.com/s/0qf06of9lp1m51d/pe_overlap.pnghttps://www.dropbox.com/s/0qf06of9lp1m51d/pe_overlap.png;cid=1368714426780-10 ) I checked for the temp. dist. which also looks fine to me . https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.pnghttps://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png;cid=1368714426780-10 I don't know why all plots are similar ?? Is this related to wrong settings in mdp file. Here's the mdp file that I am using for production run. I changed ref_t for each replica in the mdp file. define = -DPOSRESHELIX ; -DFLEXIBLE -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps nsteps = 2500; 5 ps = 50 ns nstcomm = 10 nstcalcenergy = 10 nstxout = 1000 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog = 1000 ; frequency to write energies to log file nstenergy = 1000 ; frequency to write energies to edr file vdwtype = cut-off coulombtype = cut-off pbc = no nstlist = 0 ns_type = simple rlist = 0 ; this means all-vs-all (no cut-off), which gets expensive for bigger systems rcoulomb= 0 rvdw= 0 comm-mode = angular comm-grps = system optimize_fft= yes ; V-rescale temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 tc_grps = system ref_t = 250 ; Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp= 300 gen_seed= -1 ; ; Implicit solvent ; implicit_solvent= GBSA gb_algorithm= Still ; HCT ; OBC nstgbradii = 1 rgbradii= 0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 78.5; Dielectric constant for the implicit solvent ; gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm= Ace-approximation sa_surface_tension = 0.005 I suspect that I am doing something wrong somewhere ... It will be helpful if anybody can help me in this regard... Regards -- BHARAT -- 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] the details about g_density
I have used the program g_density to generate the mass density profile and the charge density profile of molecules at gas-liquid interface. My question is: Is the center of mass/charge used by g_density to compute the the mass/charge density profile? I'm eager for the answer, because the reviewer of my submitted article ask me for that question but I don't know how to reply. I have used google to search for the answer, but I did not found. I really appreciate you for the attention and consideration to this email. Best regards, Vigar Yang Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China -- 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] NVT and NPT for small peptide
Hi, when simulation small peptideS, 6 or 10 amino acid, how long it is need for NVT and NPT? -- View this message in context: http://gromacs.5086.x6.nabble.com/NVT-and-NPT-for-small-peptide-tp5008461.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Effect of pressure coupling frequency on gpu simulations
Thanks Mark, That really helped to clarify how everything is interacting around the verlet scheme. What statistics do you recommend examining between nstpcouple settings? Pressure/box size variation is the obvious one but I was curious whether you had something else in mind. -Trayder On Thu, May 23, 2013 at 4:18 AM, Mark Abraham mark.j.abra...@gmail.comwrote: On Wed, May 22, 2013 at 6:32 AM, Trayder trayder.tho...@monash.edu wrote: Hi all, I've been running 5fs timestep simulations successfully without gpus (united-atom, HEAVYH). When continuing the same simulations on a gpu cluster utilising the verlet cutoff-scheme they crash within 20 steps. Reducing the timestep to 2fs runs smoothly, however I noticed the message: Making this change manually led to crashing simulations as nstcalclr, nsttcouple and nstpcouple default to the value of nstlist. After defining them all separately I was able to determine that the simulation exploding was dependent entirely on nstpcouple and by lowering it to 5 (from the default 10) I was able to run simulations at a 5fs timestep. So, my questions: Is lowering nstpcouple a legitimate solution or just a bandaid? P-R does not cope well with situations where the box size changes enough (e.g. you should normally avoid it during equilibration). nstpcouple != 1 means that you simulate on an NVE manifold for a period of time (maybe with some T changes if nsttcouple != nstpcouple), and I'd suppose the longer that interval the bigger the chance of a build-up of pressure that P-R will then try to relieve by changing the box size. Larger nstlist and dt will exacerbate this, of course. I would recommend you experiment and see how far you can push things and keep statistics that still resemble those with small nstpcouple. Larger nstpcouple helps reduce the frequency with which global communication occurs, and that affects your simulation rate... life is complex! It would be nice if we were able to compute heuristics so that mdrun could anticipate such a problem and warn you, but off-hand that seems a tricky problem... The simulation runs with nstcalclr and nsttcouple set to 50 along with nstcalclr should have no effect - it works only with the group scheme, which does not work on GPUs. nstlist. Is nstlist the only setting that should be increased when utilising gpus? Yes, AFAIK. The point is that nstlist is the interval between neighbour searches, and (at the moment at least) that's only done on the CPU. The Verlet kernels cheerfully compute lots of zero-strength interactions outside the cutoff (by design), and depending on the relative performance of your hardware it is normally more efficient to bump nstlist up (and rlist accordingly, to provide a larger buffer for diffusion of particles) and compute more zeroes than it is to search for neighbours more often. Mark Thanks in advance, -Trayder P.S. The working mdp file: -- View this message in context: http://gromacs.5086.x6.nabble.com/Effect-of-pressure-coupling-frequency-on-gpu-simulations-tp5008439.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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 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 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] Re: NVT and NPT for small peptide
Hi Maggin, It depend on your protein stability..It can be short or long..Check the .edr file by using g_energy On Thu, May 23, 2013 at 9:44 AM, maggin [via GROMACS] ml-node+s5086n5008461...@n6.nabble.com wrote: Hi, when simulation small peptideS, 6 or 10 amino acid, how long it is need for NVT and NPT? If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/NVT-and-NPT-for-small-peptide-tp5008461.html To start a new topic under GROMACS Users Forum, email ml-node+s5086n4370410...@n6.nabble.com To unsubscribe from GROMACS, click here. NAML -- Best Regards, Nur Syafiqah Abdul Ghani, Theoretical and Computational Chemistry Laboratory, Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor. alternative email : syafiqahabdulgh...@gmail.com @ gs33...@mutiara.upm.edu.my -- View this message in context: http://gromacs.5086.x6.nabble.com/NVT-and-NPT-for-small-peptide-tp5008461p5008463.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] renumber residue number in file topology
Dear all, I want to renumber residue number in file .top (to begin from 1). Have anyone has a script for this purpose ? Thankful for any help! Thu -- 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
