Re: [gmx-users] query on replica exchange
Hi, You can only have as many replicas as you have MPI processes available, but you can find out how to configure your MPI to allow such over-subscription of your hardware. Mark On May 31, 2013 6:28 AM, Sanku M msank...@yahoo.com wrote: Hi, I am wondering if there is a way I can use twice more number of replica than the number of CPU is available so that each replica will run at 50 % CPU usage..For example if I have 48 replica and have 24 CPUs, is it a possibility to perform Replica exchange in gromacs ? I was using gromacs4.5.4 and I could not get it worked. It works only when I had atleast equal number of Replica and CPU available. Any help will be appreciated. -- 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] Increasing performance of siumulation in cluster
Hi all, I recently ran 20ns simulation in linux cluster. Used following script for MD simulation #This is the first simulation MD.mdp file contains 20 ns setup grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_first10.tpr mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16 #This extends 10 ns simulation tpbconv -s MD_first10.tpr -o md_extended.tpr -extend 1 mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi MD_first10.cpt -append -np 16 and bsub file #!/bin/bash #BSUB -J testgromacs # the job's name/array job #BSUB -W 120:00 # max. wall clock time in hh:mm #BSUB -n 16,16 # number of processors Min,Max #BSUB -o /home/sample/output_%J.log # output file #BSUB -e /home/sample/errors_%J.log # error file #BSUB -M 8192 #Memory limit in MB echo Started at `date` echo cd /home/sample/ echo Running gromacs test in `pwd` ./MD.sh echo Finished at `date` * * * * *It ran for total 5 days but didnt give all 20ns simulation ..So i checked log file for performance * *Parallel run - timing based on wallclock.* * * * NODE (s) Real (s) (%)* * Time: 359019.178 359019.178100.0* * 4d03h43:39* * (Mnbf/s) (GFlops) (ns/day) (hour/ns)* *Performance:445.015 24.708 2.407 9.973* * * * * *It looks like this gave very performance 2.4 ns per 9 hours..this looks very low for me.. Can any body tell me how to increase performance of simulation* Thanks Nitin -- 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] Increasing performance of siumulation in cluster
There are lots of things you might do, but when we don't know what's in the simulation or anything about the hardware, nobody can tell. Mark On Thu, May 30, 2013 at 2:16 PM, Sainitin Donakonda saigr...@gmail.comwrote: Hi all, I recently ran 20ns simulation in linux cluster. Used following script for MD simulation #This is the first simulation MD.mdp file contains 20 ns setup grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_first10.tpr mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16 #This extends 10 ns simulation tpbconv -s MD_first10.tpr -o md_extended.tpr -extend 1 mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi MD_first10.cpt -append -np 16 and bsub file #!/bin/bash #BSUB -J testgromacs # the job's name/array job #BSUB -W 120:00 # max. wall clock time in hh:mm #BSUB -n 16,16 # number of processors Min,Max #BSUB -o /home/sample/output_%J.log # output file #BSUB -e /home/sample/errors_%J.log # error file #BSUB -M 8192 #Memory limit in MB echo Started at `date` echo cd /home/sample/ echo Running gromacs test in `pwd` ./MD.sh echo Finished at `date` * * * * *It ran for total 5 days but didnt give all 20ns simulation ..So i checked log file for performance * *Parallel run - timing based on wallclock.* * * * NODE (s) Real (s) (%)* * Time: 359019.178 359019.178100.0* * 4d03h43:39* * (Mnbf/s) (GFlops) (ns/day) (hour/ns)* *Performance:445.015 24.708 2.407 9.973* * * * * *It looks like this gave very performance 2.4 ns per 9 hours..this looks very low for me.. Can any body tell me how to increase performance of simulation* Thanks Nitin -- 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] Increasing performance of siumulation in cluster
Hi Mark, I forgot to mention about simulation it is protein ligand simulation which contains one protein and ligand with 2 solute molecules..and regarding hardware of cluster which is in my university as follows CPUs AMD Opteron 6274 number of cores 5888 th. peak performance 51.8 TFlops compute nodes 4-way nodes *Saxonid* with 64 cores nodes with 64 GB RAM 48 nodes with 128 GB RAM 24 nodes with 256 GB RAM 12 nodes with 512 GB RAM 8 Can you now suggest some methods which i can use to optimize to increase performance Thanks, Nitin On Fri, May 31, 2013 at 10:54 AM, Mark Abraham mark.j.abra...@gmail.comwrote: There are lots of things you might do, but when we don't know what's in the simulation or anything about the hardware, nobody can tell. Mark On Thu, May 30, 2013 at 2:16 PM, Sainitin Donakonda saigr...@gmail.com wrote: Hi all, I recently ran 20ns simulation in linux cluster. Used following script for MD simulation #This is the first simulation MD.mdp file contains 20 ns setup grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o MD_first10.tpr mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16 #This extends 10 ns simulation tpbconv -s MD_first10.tpr -o md_extended.tpr -extend 1 mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi MD_first10.cpt -append -np 16 and bsub file #!/bin/bash #BSUB -J testgromacs # the job's name/array job #BSUB -W 120:00 # max. wall clock time in hh:mm #BSUB -n 16,16 # number of processors Min,Max #BSUB -o /home/sample/output_%J.log # output file #BSUB -e /home/sample/errors_%J.log # error file #BSUB -M 8192 #Memory limit in MB echo Started at `date` echo cd /home/sample/ echo Running gromacs test in `pwd` ./MD.sh echo Finished at `date` * * * * *It ran for total 5 days but didnt give all 20ns simulation ..So i checked log file for performance * *Parallel run - timing based on wallclock.* * * * NODE (s) Real (s) (%)* * Time: 359019.178 359019.178100.0* * 4d03h43:39* * (Mnbf/s) (GFlops) (ns/day) (hour/ns)* *Performance:445.015 24.708 2.407 9.973* * * * * *It looks like this gave very performance 2.4 ns per 9 hours..this looks very low for me.. Can any body tell me how to increase performance of simulation* Thanks Nitin -- 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: g_x2top help
Hi Millinda.
I know it is an old post, bt I am not sure if your defaults are correct.
This question is only because I am struggling to make CLAYff work and hence
looking around. So mb you know something I don't.
[ defaults ]
; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5
; parameters are taken from the clay force field
The combination rule you have it is* 3*, i.e sigma epsilon with
combination rule:
C^6_{ij} = (C^6_{i C^6_j)^{1/2} and same for C^{12}_{ij}
The paper by Cygan et al, 2004 on p. 1257, shows different combination rule
(i.e *2*).
I am also not sure if there is a need for for gen-pairs, and hence FudgeLJ
and QQ. Mine are set to default value of 1.
Thanks, V
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[gmx-users] Re: umbrella sampling for two polymer interaction
Look also into the manual. But the tutorial is a nice place to start. For further comments see below: Dear Lloyd, I have read that but my system is different regards, On Thu, May 30, 2013 at 8:28 PM, lloyd riggslloyd.ri...@gmx.ch wrote: Dear Jiom, Look at justines tutorial, there's example pull .mdp. Stephan Watkins I want to do Umbrella sampling between two different polymers (A and B) interacting with each other with starting configuration separated by some distance and I am trying to bring them closer. I have some queries regarding pull inputs: (this is for to run a umbrella sampling at some distance) pull = umbrella pull_geometry = distance pull_dim = Y Y Y pull_start = ??? pull_ngroups = 2? pull_group0 = polymer_B pull_group1 = polymer_A pull_init1 = 0 pull_rate1 = 0.0 please suggest for following: 1) pull_dim I have set to Y Y Y: Is this correct I do not want to make it interact with some directional vector I don't really understand the question. If you use 'pull_dim = Y Y Y' the pulling potential acts in all 3 dimensions, if you use 'pull_dim = Y N N' the pulling potential acts only in the X direction and your two groups an move freely in the YZ-plane. 2) Which should be group0 or group1, in other words should I pull both together or how I should decide which one should be reference and which to be pulled as both are different polymers? Depends on what you want to do. Easiest way would be define one polymer a group0/reference group and the other as group1/pulled group. System shouldn't care about which polymer is which group. If you do a pulling simulation, there can be reason for chosing the groups (protein = reference , ligand = pulled group, since we want to pull it away) 3) And also what should be pull_ngroups because if there is no reference group then it should be 2 Better use a reference group - pull_ngroups = 1 You don't want to pull in absolute coordinates, when your system can rotate... 4) I am not able to understand pull_start option with pull_init1. In this case if it is set to yes and 0.0 respectively then does that mean this combination is equivalent to pull_start = No if I just assume pull_init1 does not have any default value (which is 0.0); not existing From the setup which you have written above: polymer_B is the reference group. the origin of the pulling potential is at 'pull_init1' (a length) along the vector which goes from polymer_B to polymer_A (sine you use pull_geometry = distance). If you set pull_init1=0 and pull_start=no, polymer_A will crash into polymer_B (since the origin of the umbrella potential is directly at the center of mass of polymer_B). If you set pull_init1=0 and pull_start=yes, GROMACS adds the distance between polymer_B and A to pull_init1 (- so pull_init1 is now greater than 0.0). Now the origin of the umbrella potential is at the center of mass of polymer_A. - A is restrainted to a certian distance of B. 5) Also finally where are upper and lower bounds defined. pull_k1 = 1000 is harmonic applied to some equilibrium distance value. How this distance is taken by the programme (or it is just the starting distance taken between two groups) and what are the ± values defined. (say in AMBER I define r1,r2,r3,r4; where r2=r3 which is assumed equilibrium value and r1 is lower and r4 is upper value which defines shape of potential) The umbrella potential is a simple harmonic potential (so no fancy stuff as in AMBER) with V = 1/2 k x^2 where x is the violation of the equilibrium distance. For your setup V = 1/2 (pull_init1 - distance(B-A))^2 where distance(B-A) means the distance between both polymers. Greetings Thomas -- 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: umbrella sampling for two polymer interaction
Dear Thomas, Thanks a lot for your time and nice explanation. I was not able to get specially the pull_start flag but now its quite clear. I feel sorry, that should be pull_dim = N N N in my case. Also I will be much thankful if you please can help me to make understand following: 1) If you do a pulling simulation, there can be reason for chosing the groups (protein = reference , ligand = pulled group, since we want to pull it away) This indeed is correct but I am not able to get depth of this. I mean to say lets keep ligand as a reference and protein as pulled group then yes it sounds stupid but I am not able to provide a reason myself why we can not keep ligand as reference and pull protein rather !! 2) 3) And also what should be pull_ngroups because if there is no reference group then it should be 2 Better use a reference group - pull_ngroups = 1 You don't want to pull in absolute coordinates, when your system can rotate.. I am not able to understand this part. Can you please provide some example so that it makes easier to understand this Much thanks again, regards, Jiom On Fri, May 31, 2013 at 1:21 PM, Thomas Schlesier schl...@uni-mainz.dewrote: Look also into the manual. But the tutorial is a nice place to start. For further comments see below: Dear Lloyd, I have read that but my system is different regards, On Thu, May 30, 2013 at 8:28 PM, lloyd riggslloyd.ri...@gmx.ch wrote: Dear Jiom, Look at justines tutorial, there's example pull .mdp. Stephan Watkins I want to do Umbrella sampling between two different polymers (A and B) interacting with each other with starting configuration separated by some distance and I am trying to bring them closer. I have some queries regarding pull inputs: (this is for to run a umbrella sampling at some distance) pull = umbrella pull_geometry = distance pull_dim = Y Y Y pull_start = ??? pull_ngroups = 2? pull_group0 = polymer_B pull_group1 = polymer_A pull_init1 = 0 pull_rate1 = 0.0 please suggest for following: 1) pull_dim I have set to Y Y Y: Is this correct I do not want to make it interact with some directional vector I don't really understand the question. If you use 'pull_dim = Y Y Y' the pulling potential acts in all 3 dimensions, if you use 'pull_dim = Y N N' the pulling potential acts only in the X direction and your two groups an move freely in the YZ-plane. 2) Which should be group0 or group1, in other words should I pull both together or how I should decide which one should be reference and which to be pulled as both are different polymers? Depends on what you want to do. Easiest way would be define one polymer a group0/reference group and the other as group1/pulled group. System shouldn't care about which polymer is which group. If you do a pulling simulation, there can be reason for chosing the groups (protein = reference , ligand = pulled group, since we want to pull it away) 3) And also what should be pull_ngroups because if there is no reference group then it should be 2 Better use a reference group - pull_ngroups = 1 You don't want to pull in absolute coordinates, when your system can rotate... 4) I am not able to understand pull_start option with pull_init1. In this case if it is set to yes and 0.0 respectively then does that mean this combination is equivalent to pull_start = No if I just assume pull_init1 does not have any default value (which is 0.0); not existing From the setup which you have written above: polymer_B is the reference group. the origin of the pulling potential is at 'pull_init1' (a length) along the vector which goes from polymer_B to polymer_A (sine you use pull_geometry = distance). If you set pull_init1=0 and pull_start=no, polymer_A will crash into polymer_B (since the origin of the umbrella potential is directly at the center of mass of polymer_B). If you set pull_init1=0 and pull_start=yes, GROMACS adds the distance between polymer_B and A to pull_init1 (- so pull_init1 is now greater than 0.0). Now the origin of the umbrella potential is at the center of mass of polymer_A. - A is restrainted to a certian distance of B. 5) Also finally where are upper and lower bounds defined. pull_k1 = 1000 is harmonic applied to some equilibrium distance value. How this distance is taken by the programme (or it is just the starting distance taken between two groups) and what are the ą values defined. (say in AMBER I define r1,r2,r3,r4; where r2=r3 which is assumed equilibrium value and r1 is lower and r4 is upper value which defines shape of potential) The umbrella potential is a simple harmonic potential (so no fancy stuff as in AMBER) with V = 1/2 k x^2 where x is the violation of the equilibrium distance. For your setup V = 1/2 (pull_init1 - distance(B-A))^2 where distance(B-A) means the distance between both polymers. Greetings Thomas -- gmx-users mailing list
[gmx-users] namd2gmx topology conversion tool
Dear Gromacs users! I have some topologies made for NAMD (param files) which I'd like convert to the Gromacs itp formats. Could someone provide me with some tools for such conversion? Thanks for help, James -- 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] Dihedral Autocorrelation Function with negative values
Dear gmx users, I am writing to ask why I am getting a dihedral autocorrelation function (ACF) with negative values. I am trying to calculate the ACF using g_angle (gromacs 4.5.5) with the following set of flags: g_angle -f trajectory.xtc -type dihedral -oc acf.xvg -od angdist.xvg -n angle.ndx The ACF starts from 1 as expected and slowly drops (sometimes) to values below 0 (approx. -0.2). Even when I use the flag -normalize (which I would expect normalizes the ACF between 0 and 1) the output is identical. Can you please help me to figure out why this happens? Any help will be very much appreciated. Thank you in advance. Cheers, David -- 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] oxidized lipid - Peroxidated lipid
Hi All, Does anybody know which force filed I can use for oxidized lipid or peroxidated lipid? You can see the below link to get how fatty acid will change by peroxidation: http://en.wikipedia.org/wiki/Lipid_peroxidation If there is not any, what is the suggestion? Thanks, Dariush -- View this message in context: http://gromacs.5086.x6.nabble.com/oxidized-lipid-Peroxidated-lipid-tp5008661.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] Vritual Sites and simulation time-step
3) Also I've already performed small simulation with the time step 5 fs (defining virtual sites by means of pdb2gmx -vsites and introducing heavy hydrogens. I've not observed any errors during my simulation. When I've tried to increase dt up to 7 fs I've obtained warnings according to that I should increase tau_p (from 2 ps with Parinello coupling). How tau_p is relevant to the timestep and when I could obtain more information about such constants ? E.g if i increase tau_p doest it means that I provide weaker coupling to the system with pressure bath ? (higher constant- higher relaxation times ) James 2013/5/30 James Starlight jmsstarli...@gmail.com Also some questions about corrections in the mdp besides the time-step file which should be included with the VS. 1) What constrains algorithm should I use ? typically I use ; Bond parameters constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy 2) Should I vary tau_t constant assuming that I use SD integrator as the thermostat ( I'm using 2 ps ) ? 2013/5/30 James Starlight jmsstarli...@gmail.com Mark, thanks for advise. As I understood for the usage of virtual sites in typical protein-water system I should (1) define all hydrogens as the virtual atoms (2) increase atom masses of the hydrogens presented in the water, COOH NH2 OH and SH as well as polar groups (3) make virtual sites for the angles and dihedrals of peptide bond as well as sidechains. Also I've noticed that (1) and (2) can be done with the pdb2gmx with options -vsite and -heavyh respectfully. From this point its not quite clear for me (1) should I make some corrections in topology for dihedrals? In the manual 6.7 I've found some suggestions for the dihedrals of the different functional groups. (2) should I define VSITES for solvent molecules filled into the box by the genbox ? (3) As I understood the inclusion of the VSITES for hydrogens would allow me to increase timestep up to 5-8fs. What possible negative side-effects of the inclusion of VSITES might occur in simulation ? James 2013/5/30 Mark Abraham mark.j.abra...@gmail.com Manual 6.7? On Thu, May 30, 2013 at 7:05 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs users! In some discussions I've noticed that people told about usage of virtual sites which allow to increase time step of the simulation of such systems. From manual and tutorial its not quite understand for me how with inclusion of such dummy atoms (which can be used to reduce number of atoms of the some solvent-like molecule or to mimic electron pairs in the water for instance) influence on time-step can be achieved ? James -- 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
Re: [gmx-users] Dihedral Autocorrelation Function with negative values
On 2013-05-31 15:59, Davide Mercadante wrote: Dear gmx users, I am writing to ask why I am getting a dihedral autocorrelation function (ACF) with negative values. I am trying to calculate the ACF using g_angle (gromacs 4.5.5) with the following set of flags: g_angle -f trajectory.xtc -type dihedral -oc acf.xvg -od angdist.xvg -n angle.ndx The ACF starts from 1 as expected and slowly drops (sometimes) to values below 0 (approx. -0.2). Even when I use the flag -normalize (which I would expect normalizes the ACF between 0 and 1) the output is identical. Can you please help me to figure out why this happens? Any help will be very much appreciated. Thank you in advance. Cheers, David Because the angle between the two planes can become 180 in which case the dot product is negative. In the long run it should go to zero. It is described in D. van der Spoel and H.J.C. Berendsen: Molecular dynamics simulations of Leu-Enkephalin in water and DMSO Biophys. J. 72 pp. 2032-2041 (1997) -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] OPLS-AA to CHARMM conversion in gromacs ffnonbonded.itp
Dear All, I have a little confusion with the non-bonding parameters conversion from OPLS-AA to CHARMM in gromacs. If I see the ffnonbonded.itp in both the cases I get the following numbers OPLS-GROMACS Sigma = 0.1644471 nm Epsilon = (0.875044*4.184) = 3.66118 kJ/mol . CHARMM-GROMACS Sigma = 0.21114299 nm Epsilon = 0.06276 kJ/mol Now, from the charmm27 parameters file I get CHARMM27 Rmin/2 = 1.18500 Ang Epsilon = -0.0150 kcal/mol Converting these charmm parameters to gromacs formate I have to do following conversions Sigma = 2^(5/6) * (Rmin/2) = 2^(5/6) * 1.185 = 2.1114299 Ang = 0.2114299 nm Epsilon = 0.0150 * 4.184 = 0.06276 kJ/mol So, CHARMM (par_water_ions.prm) to charmm(ffnonbonded.itp) is fine. But the problem I'm facing to convert the OPLS(ffnonbonded.itp) to CHARMM(ffnonbonded.itp). I apologize for making any confusion. Thanks, Tarak -- 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: OPLS-AA to CHARMM conversion in gromacs ffnonbonded.itp
All these parameters are for Mg2+, forgot to mention. On Fri, May 31, 2013 at 10:48 PM, tarak karmakar tarak20...@gmail.comwrote: Dear All, I have a little confusion with the non-bonding parameters conversion from OPLS-AA to CHARMM in gromacs. If I see the ffnonbonded.itp in both the cases I get the following numbers OPLS-GROMACS Sigma = 0.1644471 nm Epsilon = (0.875044*4.184) = 3.66118 kJ/mol . CHARMM-GROMACS Sigma = 0.21114299 nm Epsilon = 0.06276 kJ/mol Now, from the charmm27 parameters file I get CHARMM27 Rmin/2 = 1.18500 Ang Epsilon = -0.0150 kcal/mol Converting these charmm parameters to gromacs formate I have to do following conversions Sigma = 2^(5/6) * (Rmin/2) = 2^(5/6) * 1.185 = 2.1114299 Ang = 0.2114299 nm Epsilon = 0.0150 * 4.184 = 0.06276 kJ/mol So, CHARMM (par_water_ions.prm) to charmm(ffnonbonded.itp) is fine. But the problem I'm facing to convert the OPLS(ffnonbonded.itp) to CHARMM(ffnonbonded.itp). I apologize for making any confusion. Thanks, Tarak -- 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: umbrella sampling for two polymer interaction
For comments to your questions see below. More general: (somewhat longer than i wanted. Hope you find some answers here) Imagine two interacting particles A and B which are alinged to the x-axis. We take A as the reference group, B as pulled group and put the origin of the umbrella potential on top of B (pull_start=yes). Simulation starts - A and B moves. Pull-code step: From A we calculate the new position of the umbrella potential, this is unequal to B, since B moved and our reference point move. Now we have a force acting on B, 'pull_dim' controls in which directions the force acts. With 'Y Y Y' B is pulled towards the origin of the umbrella potential (and with this to the position it should have relative to A). If one uses only 'Y N N' B would only move along the x-axis due to the pull, but could move freely in the yz-plane. In the end one would get a structure where A and B have the right distance in the x-axis but are miles away from each other in the yz-plane. Now imagine we pull B away from A. Since MD simulations normally separete the movement of the center of mass of the system, it would look like A and B would move away from a middle point. (Interchanging A and B should give the same results). Think in your case (doing umbrella sampling) the mdp-file you suggested would be most appropiate (with 'pull_start=yes' and 'pull_ngroups=1'). This gives you a potential which fixes the distance between the two proteins. One thing you should be aware is that if you restrain the distance in 3d, you have to account for entropic effects (see also the GROMACS manual). If you restrain the system only in one direction, these don't arise. Think this is the reason why one sees some work with umbrella sampling were the restraint works only in one direction. Am 31.05.2013 17:20, schrieb gmx-users-requ...@gromacs.org: Dear Thomas, Thanks a lot for your time and nice explanation. I was not able to get specially the pull_start flag but now its quite clear. I feel sorry, that should be pull_dim = N N N in my case. Also I will be much thankful if you please can help me to make understand following: STOP!!! You never want to use the pull-code and 'pull_dim = N N N' This would mean that there is no force acting between your two groups. Then one could have skipped using the pull-code... 1) If you do a pulling simulation, there can be reason for chosing the groups (protein = reference , ligand = pulled group, since we want to pull it away) This indeed is correct but I am not able to get depth of this. I mean to say lets keep ligand as a reference and protein as pulled group then yes it sounds stupid but I am not able to provide a reason myself why we can not keep ligand as reference and pull protein rather !! Think this setup should also work. For some simple systems i imagine it should give identical results. For complex system i would also think so. But i can't comment on this with actual expirience. The dimer systems which i investigated were symmetric... 2) 3) And also what should be pull_ngroups because if there is no reference group then it should be 2 Better use a reference group - pull_ngroups = 1 You don't want to pull in absolute coordinates, when your system can rotate.. I am not able to understand this part. Can you please provide some example so that it makes easier to understand this Imagine only a single protein which you want to unfold. In an equilibrium simulation the protein can freely rotate in the box. If we use the N-terminus as the reference group and the C-terminus a the pulled group, the origin of the umbrella potential will always be updated and will account for movement of the N-terminus (reference group). If one would pull in absolute coordinates, one would need to give the position of the umbrella potential in absolute space. The molecule can move, but the origin of the potential will always stay fixed at one place. Think in the end this would be equal to an position restraint of said group. If one would want to restrain the distance of two groups in such a way, one would need two umbrella potentials. But since these would be equal to two position restraints, there would be no coupling between the two. I mean, if both groups move around but would have the same distance it should be ok since the distance is fine. But both umbrella potential would pull each group back to the initial position. Much thanks again, regards, Jiom On Fri, May 31, 2013 at 1:21 PM, Thomas Schlesierschl...@uni-mainz.dewrote: Look also into the manual. But the tutorial is a nice place to start. For further comments see below: Dear Lloyd, I have read that but my system is different regards, On Thu, May 30, 2013 at 8:28 PM, lloyd riggslloyd.ri...@gmx.ch wrote: Dear Jiom, Look at justines tutorial, there's example pull .mdp. Stephan Watkins I want to do Umbrella sampling between two different
[gmx-users] Nose-Hover chains for membrane protein simulation
Dear Gromacs users! I'd like to perform simulation of the membrane protein in lipid-water system using Nose-Hover with chains. From manual I've found that with such thermostat I should use (1) md-vv integrator (2) MTTK instead of Parinello's batostat and (3) shake instead of LINCS. How doest such options compatible with the simulation of membrane proteins in general ? On what other options should I pay attention during simulation of membrane protein with NH chains ? Thanks for help, James -- 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: umbrella sampling for two polymer interaction
Dear Thomas, Thanks a lot again for great reply. Please clarify this also, If one uses only 'Y N N' B would only move along the x-axis due to the pull, but could move freely in the yz-plane You never want to use the pull-code and 'pull_dim = N N N' This would mean that there is no force acting between your two groups. Then one could have skipped using the pull-code... So keeping Y N N will allow free movement in yz plane. So if I want A B to move freely in xyz but just keep them separated by some distance with spring const (just like two balloons tied to each other flying in air). Sorry confused. In AMBER I remember I did once methane-methane interaction, just distance based umbrella sampling. But there I did not provide any direction. So should it not be N N N in Gromacs if I want to allow them freely move in xyz. thanks, On Fri, May 31, 2013 at 8:53 PM, Thomas Schlesier schl...@uni-mainz.dewrote: For comments to your questions see below. More general: (somewhat longer than i wanted. Hope you find some answers here) Imagine two interacting particles A and B which are alinged to the x-axis. We take A as the reference group, B as pulled group and put the origin of the umbrella potential on top of B (pull_start=yes). Simulation starts - A and B moves. Pull-code step: From A we calculate the new position of the umbrella potential, this is unequal to B, since B moved and our reference point move. Now we have a force acting on B, 'pull_dim' controls in which directions the force acts. With 'Y Y Y' B is pulled towards the origin of the umbrella potential (and with this to the position it should have relative to A). If one uses only 'Y N N' B would only move along the x-axis due to the pull, but could move freely in the yz-plane. In the end one would get a structure where A and B have the right distance in the x-axis but are miles away from each other in the yz-plane. Now imagine we pull B away from A. Since MD simulations normally separete the movement of the center of mass of the system, it would look like A and B would move away from a middle point. (Interchanging A and B should give the same results). Think in your case (doing umbrella sampling) the mdp-file you suggested would be most appropiate (with 'pull_start=yes' and 'pull_ngroups=1'). This gives you a potential which fixes the distance between the two proteins. One thing you should be aware is that if you restrain the distance in 3d, you have to account for entropic effects (see also the GROMACS manual). If you restrain the system only in one direction, these don't arise. Think this is the reason why one sees some work with umbrella sampling were the restraint works only in one direction. Am 31.05.2013 17:20, schrieb gmx-users-requ...@gromacs.org: Dear Thomas, Thanks a lot for your time and nice explanation. I was not able to get specially the pull_start flag but now its quite clear. I feel sorry, that should be pull_dim = N N N in my case. Also I will be much thankful if you please can help me to make understand following: STOP!!! You never want to use the pull-code and 'pull_dim = N N N' This would mean that there is no force acting between your two groups. Then one could have skipped using the pull-code... 1) If you do a pulling simulation, there can be reason for chosing the groups (protein = reference , ligand = pulled group, since we want to pull it away) This indeed is correct but I am not able to get depth of this. I mean to say lets keep ligand as a reference and protein as pulled group then yes it sounds stupid but I am not able to provide a reason myself why we can not keep ligand as reference and pull protein rather !! Think this setup should also work. For some simple systems i imagine it should give identical results. For complex system i would also think so. But i can't comment on this with actual expirience. The dimer systems which i investigated were symmetric... 2) 3) And also what should be pull_ngroups because if there is no reference group then it should be 2 Better use a reference group - pull_ngroups = 1 You don't want to pull in absolute coordinates, when your system can rotate.. I am not able to understand this part. Can you please provide some example so that it makes easier to understand this Imagine only a single protein which you want to unfold. In an equilibrium simulation the protein can freely rotate in the box. If we use the N-terminus as the reference group and the C-terminus a the pulled group, the origin of the umbrella potential will always be updated and will account for movement of the N-terminus (reference group). If one would pull in absolute coordinates, one would need to give the position of the umbrella potential in absolute space. The molecule can move, but the origin of the potential will always stay fixed at one place. Think in the end this would be equal to an position restraint of said
[gmx-users] Domain Decomposition Error
Hi Everyone, I'm trying to run energy minimization on my system and I am encountering the following error: Getting Loaded... Reading file em.tpr, VERSION 4.5.5 (single precision) Starting 16 threads Loaded with Money Will use 10 particle-particle and 6 PME only nodes This is a guess, check the performance at the end of the log file --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 6436 Fatal error: There is no domain decomposition for 10 nodes that is compatible with the given box and a minimum cell size of 9.07242 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I've tested my bash script on a local server with an i7 and I've been able to run error free, however when running on xsede resources I continually encounter this error. For information here is my bash: #minimization grompp -f minim.mdp -c protein_solv_ions.gro -p protein.top -o em.tpr mdrun -v -deffnm em if [ ! $? == 0 ] then echo ERROR - Energy minimization exit 5 fi and Here is my minim.mdp integrator = steep emtol = 10 emstep = 0.01 nsteps = 200 energygrps = System nstlist= 5 ns_type= grid rlist = 1.0 coulombtype= PME rcoulomb = 1.0 rvdw = 1.0 pbc= xyz Any input would help! Thanks, Parker -- 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] Increasing performance of siumulation in cluster
On Fri, May 31, 2013 at 11:30 AM, Sainitin Donakonda saigr...@gmail.comwrote: Hi Mark, I forgot to mention about simulation it is protein ligand simulation which contains one protein and ligand with 2 solute molecules.. So assuming you mean solvent, about 60K atoms. and regarding hardware of cluster which is in my university as follows CPUs AMD Opteron 6274 number of cores 5888 th. peak performance 51.8 TFlops compute nodes 4-way nodes *Saxonid* with 64 cores nodes with 64 GB RAM 48 nodes with 128 GB RAM 24 nodes with 256 GB RAM 12 nodes with 512 GB RAM 8 Links are better than copy-and-paste... https://doc.zih.tu-dresden.de/hpc-wiki/bin/view/Compendium/HardwareAtlas Can you now suggest some methods which i can use to optimize to increase performance Your hardware is quite useful. You should be getting better performance. Exactly how to do that depends on the simulation (e.g. PME or not, group or Verlet kernels). You should start with http://www.gromacs.org/Documentation/Acceleration_and_parallelization and experiment with the balance of MPI processes and OpenMP threads per node of your hardware. Look at the timing breakdown at the end of the .log file, and pay attention to all the information grompp and mdrun writes! 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] Domain Decomposition Error
Could be a bug, but unless you can reproduce it with 4.5.7 or 4.6.x then you won't get much help there :-) Mark On Fri, May 31, 2013 at 9:56 PM, Parker de Waal parker.dewaa...@kzoo.eduwrote: Hi Everyone, I'm trying to run energy minimization on my system and I am encountering the following error: Getting Loaded... Reading file em.tpr, VERSION 4.5.5 (single precision) Starting 16 threads Loaded with Money Will use 10 particle-particle and 6 PME only nodes This is a guess, check the performance at the end of the log file --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 6436 Fatal error: There is no domain decomposition for 10 nodes that is compatible with the given box and a minimum cell size of 9.07242 nm Change the number of nodes or mdrun option -rdd Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I've tested my bash script on a local server with an i7 and I've been able to run error free, however when running on xsede resources I continually encounter this error. For information here is my bash: #minimization grompp -f minim.mdp -c protein_solv_ions.gro -p protein.top -o em.tpr mdrun -v -deffnm em if [ ! $? == 0 ] then echo ERROR - Energy minimization exit 5 fi and Here is my minim.mdp integrator = steep emtol = 10 emstep = 0.01 nsteps = 200 energygrps = System nstlist= 5 ns_type= grid rlist = 1.0 coulombtype= PME rcoulomb = 1.0 rvdw = 1.0 pbc= xyz Any input would help! Thanks, Parker -- 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] OPLSAA.ff
Dear Gromacs users, I am a new user and I have some questions I confused about indexing. in atomtypes.atp clearly we can know the index is for what kind of atom but in ffbondedtype.itp there is different kind of the indexing so I confused how do i pathch the force field . Some are obvious (OH, is oxygen bonden to hydrogen and HO is a hydrogen bonded to oxygen) but definitively I dont know what type of bond makes the carbon atoms like C_2, C_3 or C * Can somebody help me what represents in ffbonded.atp. for example : opls_083 means S in RSR , opls_091 means CH2 in RCH2SR but what type of atoms are C*, C_2, C_3 , CT, CM, CS, LP, CT_2, CT_3, CW, NB etc. could you please provide me idea or list for that if somebody have. Thanks In Oplsaa.ff the indexing is as follows : atomtypes.atp opls_079 1.00800 ; H(O) ALCOHOLS JPC,90,1276 (1986) opls_080 15.03500 ; CH3 IN METHANOL JPC,90,1276 (1986) opls_081 14.02700 ; CH2 IN ETHANOL JPC,90,1276 (1986) opls_082 32.06000 ; S IN H2S JPC,90,6379 (1986) opls_083 32.06000 ; S IN RSH JPC,90,6379 (1986) opls_084 32.06000 ; S IN RSR JPC,90,6379 (1986) opls_085 32.06000 ; S IN RSSR JPC,90,6379 (1986) opls_086 1.00800 ; H IN H2S JPC,90,6379 (1986) opls_087 1.00800 ; H(S) IN RSH JPC,90,6379 (1986) opls_088 15.03500 ; CH3 IN CH3SH JPC,90,6379 (1986) opls_089 14.02700 ; CH2 IN CH3CH2SH JPC,90,6379 (1986) opls_090 15.03500 ; CH3 IN CH3SR JPC,90,6379 (1986) opls_091 14.02700 ; CH2 IN RCH2SR JPC,90,6379 (1986 The ffbonded.itp is as follows ; Some esoteric OPLS atomtypes are not freely available (or depreciated). ; Interaction types involving these have been commented out. [ bondtypes ] ; ij func b0 kb OWHW 10.09572 502080.0 ; For TIP4F Water - wlj 1/98 OWLP 10.01750 753120.0 ; -idem- C*HC 10.10800 284512.0 ; C C3 10.15220 265265.6 ; END C_2 C3 10.15220 265265.6 ; END C_3 C3 1 0.15220 265265.6 ; END C CA 10.14900 334720.0 ; wlj 8/97 C_2 CA 10.14900 334720.0 ; wlj 8/97 C_3 CA 10.14900 334720.0 ; wlj 8/97 C CB 10.14190 374049.6 ; GUA C_2 CB 10.14190 374049.6 ; GUA C_3 CB 10.14190 374049.6 ; GUA C CM 10.14440 343088.0 ; THY C_2 CM 10.14440 343088.0 ; THY C_3 CM 10.14440 343088.0 ; THY C CS 1 0.14900 334720.0 ; C_2 CS 10.14900 334720.0 ; C_3 CS 10.14900 334720.0 ; C CT 10.15220 265265.6 ; C_2 CT 10.15220 265265.6 ; C_3 CT 10.15220 265265.6 ; C CT_21 0.15220 265265.6 ; AA Calpha C_3 CT_210.15220 265265.6 ; AA C-term NOON 10.12250 460240.0 ; wlj nitro CSCW 1 0.13670 456892.8 ; wj/nm CSCS 10.14240 392459.2 ; -idem- CSCB 10.14240 392459.2 ; -idem- CSHA 10.10800 307105.6 ; -idem- CUNB 10.13200 343088.0 ; -idem- CUCA 10.14210 392459.2 ; -idem- CUHA 10.10800 307105.6 ; -idem- NANB 10.13490 334720.0 ; -idem- OSNB 1 0.13990 386601.6 ; -idem- OSCR 10.13570 386601.6 ; -idem- C3C3 10.15260 217568.0 ; Ethane C!C! 10.14600 322168.0 ; wlj C!CS 10.14600 322168.0 ; wlj -- 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] Viscosity
Hello to everyone. In version 4.5.5, calculating the viscosity with the command g_energy -vis, the generated files (eviscoi.xvg, eviscoi.xvg and visco.xvg) are inconsistent. The file evisco.xvg, for example, gives a value of zero for viscosity using the Einstein relation. Another question in 4.0.7, the file eviscoi.xvg is approximately a straight line, whereas in version 4.5.5 not. Why the Gromacs 4.0.7 gives the result in this way? Evidently, there is an inconsistency in these different results. Help me, please. -- 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] OPLSAA.ff
The conversion is in ffnonbonded.itp. However, unless you plan to modify the forcefield you shouldn't need this. Richard On 01/06/2013 00:57, Hari Pandey hariche...@yahoo.com wrote: Dear Gromacs users, I am a new user and I have some questions I confused about indexing. in atomtypes.atp clearly we can know the index is for what kind of atom but in ffbondedtype.itp there is different kind of the indexing so I confused how do i pathch the force field . Some are obvious (OH, is oxygen bonden to hydrogen and HO is a hydrogen bonded to oxygen) but definitively I dont know what type of bond makes the carbon atoms like C_2, C_3 or C * Can somebody help me what represents in ffbonded.atp. for example : opls_083 means S in RSR , opls_091 means CH2 in RCH2SR but what type of atoms are C*, C_2, C_3 , CT, CM, CS, LP, CT_2, CT_3, CW, NB etc. could you please provide me idea or list for that if somebody have. Thanks In Oplsaa.ff the indexing is as follows : atomtypes.atp opls_0791.00800 ; H(O) ALCOHOLS JPC,90,1276 (1986) opls_080 15.03500 ; CH3 IN METHANOL JPC,90,1276 (1986) opls_081 14.02700 ; CH2 IN ETHANOLJPC,90,1276 (1986) opls_082 32.06000 ; S IN H2SJPC,90,6379 (1986) opls_083 32.06000 ; S IN RSHJPC,90,6379 (1986) opls_084 32.06000 ; S IN RSRJPC,90,6379 (1986) opls_085 32.06000 ; S IN RSSR JPC,90,6379 (1986) opls_0861.00800 ; H IN H2SJPC,90,6379 (1986) opls_0871.00800 ; H(S) IN RSH JPC,90,6379 (1986) opls_088 15.03500 ; CH3 IN CH3SH JPC,90,6379 (1986) opls_089 14.02700 ; CH2 IN CH3CH2SH JPC,90,6379 (1986) opls_090 15.03500 ; CH3 IN CH3SR JPC,90,6379 (1986) opls_091 14.02700 ; CH2 IN RCH2SR JPC,90,6379 (1986 The ffbonded.itp is as follows ; Some esoteric OPLS atomtypes are not freely available (or depreciated). ; Interaction types involving these have been commented out. [ bondtypes ] ; ij func b0 kb OWHW 10.09572 502080.0 ; For TIP4F Water - wlj 1/98 OWLP 10.01750 753120.0 ; -idem- C*HC 10.10800 284512.0 ; C C3 1 0.15220 265265.6 ; END C_2 C3 10.15220 265265.6 ; END C_3 C3 10.15220 265265.6 ; END C CA 1 0.14900 334720.0 ; wlj 8/97 C_2 CA 10.14900 334720.0 ; wlj 8/97 C_3 CA 10.14900 334720.0 ; wlj 8/97 C CB 10.14190 374049.6 ; GUA C_2 CB 10.14190 374049.6 ; GUA C_3 CB 10.14190 374049.6 ; GUA C CM 1 0.14440 343088.0 ; THY C_2 CM 10.14440 343088.0 ; THY C_3 CM 10.14440 343088.0 ; THY C CS 10.14900 334720.0 ; C_2 CS 10.14900 334720.0 ; C_3 CS 1 0.14900 334720.0 ; C CT 10.15220 265265.6 ; C_2 CT 10.15220 265265.6 ; C_3 CT 10.15220 265265.6 ; C CT_21 0.15220 265265.6 ; AA Calpha C_3 CT_210.15220 265265.6 ; AA C-term NOON 10.12250 460240.0 ; wlj nitro CSCW 10.13670 456892.8 ; wj/nm CSCS 10.14240 392459.2 ; -idem- CSCB 10.14240 392459.2 ; -idem- CS HA 10.10800 307105.6 ; -idem- CUNB 10.13200 343088.0 ; -idem- CUCA 10.14210 392459.2 ; -idem- CU HA 10.10800 307105.6 ; -idem- NANB 10.13490 334720.0 ; -idem- OSNB 10.13990 386601.6 ; -idem- OS CR 10.13570 386601.6 ; -idem- C3C3 10.15260 217568.0 ; Ethane C!C! 10.14600 322168.0 ; wlj C! CS 10.14600 322168.0 ; wlj -- 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: Nose-Hover chains for membrane protein simulation
Performing 5ns simulation after 2 ns equilibration in NPT ensemble (MTTK barostat 5ps coupling ) I've observed non-physical behaviour of my system with the constant drift of the protein molecule as the rigid body in the y-z plane Energy Average Err.Est. RMSD Tot-Drift --- Pressure -760.137 --193.776218.059 (bar) From manual I've noticed that MMTK doest not support *semiisotropic scalling. *Doest it means that with the Nose-hover chains and md-vv I should use only weaker coupling during productions runs (I cant use Parinello;s barostat with such options too) Thanks for help James 2013/5/31 James Starlight jmsstarli...@gmail.com Dear Gromacs users! I'd like to perform simulation of the membrane protein in lipid-water system using Nose-Hover with chains. From manual I've found that with such thermostat I should use (1) md-vv integrator (2) MTTK instead of Parinello's batostat and (3) shake instead of LINCS. How doest such options compatible with the simulation of membrane proteins in general ? On what other options should I pay attention during simulation of membrane protein with NH chains ? Thanks for help, James -- 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
