Re: [gmx-users] position restraint
One quick observation-- you mention the filename as posre_ion.itp, but are using ion_posre.itp at #include. -g On Thu, Aug 22, 2013 at 4:24 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: Hi, I want to put position restraint on an ion , First made an .itp file of the ion: posre_ion.itp Then added these line to top file: #include ./charmm36-modified.ff/ions.itp #ifdef POSRES_ION #include ion_posre.itp #endif And added the line to mdp file define = -DPOSRES_ION But the grompp failed because it gives me the fatal error that the include line is not in the correct position. Would you please let me know if the inclusion of posre_ion.itp is not as I did? What's the problem? Thanks in advance for your suggesions. Sincerely, Shima -- 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 -- Gaurav Goel, PhD Assistant Professor Department of Chemical Engineering Indian Institute of Technology, Delhi Hauz Khas, New Delhi 110016 India -- 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] TRACE OF RMSD COMPARISON MATRIX
Following link might be helpful: http://orbeckst.github.io/GromacsWrapper/gromacs/core/fileformats/xpm.html -g -- Gaurav Goel Assistant Professor Department of Chemical Engineering Indian Institute of Technology, Delhi Hauz Khas, New Delhi 110016 India On 02-Jul-2013, at 10:45 AM, Richa Singh richa.s.rathor...@gmail.com wrote: Hello users, I'm using g_rms to compare my actual trajectory obtained from simulation with the filtered trajectory (along given set of eigenvectors), this gives me an RMSD comparison matrix in xpm format where the values of the plot are not clear. Is there any way which can help me to get the values along the diagonal of the matrix? the command that i followed is: g_rms -s ref.tpr -f actual.xtc -f2 filtered.xtc -m rmsd.xpm I want to calculate the trace of the matrix basically. Regards.. -- 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] MD simulation with varying pH
Dear Peterson, There's no magic wand for this. You'll need to find out pKa values of titrable amino acids in your protein (in literature, MEAD software, etc.). Then, you can protonate (pHpKa) / deprotonate (pHpKa) those group according to the pH. -G On Thu, Jul 5, 2012 at 12:33 PM, J Peterson think_bey...@aol.com wrote: Dear GROMACS Users, I'm planning to work on a protein that activates itself under lower pH conditions. And I don't have any clues how to do it in GROMACS. My first question is about the possibilities to do this in GROMACS, has anyone done this before? It can even be a constant simulations at a particular lower/higher pH or gradually lowering/increasing pH. Any suggestion on this would give me a lead. Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/MD-simulation-with-varying-pH-tp4999095.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 * Only plain text messages are allowed! * 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 -- Gaurav Goel, PhD Assistant Professor Department of Chemical Engineering Indian Institute of Technology, Delhi Hauz Khas, New Delhi 110016 India -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Is GPU GTX 560 compatible with GROMACS?
Dear Shouliang, Thanks. Maybe the developers can help undertand why GTX560 is not included on the GPU compatibility list for GROMACS? -G 2012/4/16 shouliang dong shouliangd...@gmail.com: It is compatible with GROMACS. 在 2012年4月14日 上午11:32，Gaurav Goel gauravgoel...@gmail.com写道： Dear All, Can you please guide me on how to find out if GeForce GTX 560 GPU card by NVIDIA will be compatible with GROMACS? On the website GTX 560 Ti is mentioned, but GTX 560 is not. Thanks, G -- Gaurav Goel, PhD Assistant Professor Department of Chemical Engineering Indian Institute of Technology, Delhi Hauz Khas, New Delhi 110016 India -- 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 -- Gaurav Goel, PhD Assistant Professor Department of Chemical Engineering Indian Institute of Technology, Delhi Hauz Khas, New Delhi 110016 India -- 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] Is GPU GTX 560 compatible with GROMACS?
Dear All, Can you please guide me on how to find out if GeForce GTX 560 GPU card by NVIDIA will be compatible with GROMACS? On the website GTX 560 Ti is mentioned, but GTX 560 is not. Thanks, G -- Gaurav Goel, PhD Assistant Professor Department of Chemical Engineering Indian Institute of Technology, Delhi Hauz Khas, New Delhi 110016 India -- 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] Nonequilibrium MD- implementing a temperature gradient simulation
My aim is to establish a temperature gradient in the MD simulation box. I'm simulating a magnesium silicate system with interatomic potentials (Mg-Mg, Mg-Si, etc.) and no bond or angle potentials. My algorithm: 1. Divide the MD box in 12 slabs along the x-axis. 2. Pick slab 3 as my source and slab 9 as sink. 3. Find the atom with highest kinetic energy in slab 3 and the atom with lowest KE in slab 9 (I amke sure both atoms have same type and hence same mass) 4. Exchange their velocity vectors. I achieve this by making following changes to the update.c routine: **In static void do_update_md( *I comment out the position update line. v[n][d]= vb; /*xprime[n][d] = x[n][d]+vb*dt;*/ *then I exchange velocities as mentioned above *and now I update the positions based on these new velocities: xprime[n][d] = x[n][d]+v[n][d]*dt; --- I print out the kinetic energy of atoms before and after exchanging and see no problem there. Total KE of these two atoms is the same before and after. But, over the length of my simulation I see average temperature of the system keeps on increasing in the NVE ensemble-- in 1ns temperature of the system increased from 3000K - 3500K. Note that the average temperature does not increase in the equilibrium NVE with same '.mdp' parameters (no velocity exchange). Any thoughts? Thanks, Gaurav -- 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] Speeding up simulation
Large cut-offs can bring artificial artifacts. e.g. *Chemical Physics Letters*http://www.sciencedirect.com/science/journal/00092614 Volume 406, Issues 1-3http://www.sciencedirect.com/science?_ob=PublicationURL_tockey=%23TOC%235231%232005%23995939998%23591997%23FLA%23_cdi=5231_pubType=Jview=c_auth=y_acct=C62818_version=1_urlVersion=0_userid=6325866md5=51f91ba17c3ce282da206786a17d50d5, 23 April 2005, Pages 49-53 -Gaurav On Wed, Aug 18, 2010 at 12:04 PM, sapna sarupria sapna.sarup...@gmail.comwrote: That might actually be the best approach speed wise. But it depends on what level of accuracy you wish for your calculations. What is your system like? May be you can have a large cut off but you will have to see what the trade off between speed and accuracy is. On Wed, Aug 18, 2010 at 10:26 AM, ms deviceran...@gmail.com wrote: On 17/08/10 22:36, Justin A. Lemkul wrote: There is no way to limit PME to certain ranges. It is a method for solving infinite sums. Usually PME is a poor choice for in vacuo simulations and the like, since there's nothing to be done for most of the simulation box. This interests me -I've used simple cut-off for in vacuo tests, but I still hadn't made my mind on what electrostatic model I should truly use. Do you have any suggestion? thanks, M. You may want to see how others (in the literature) deal with droplet-type simulations. -Justin Thanks for your help. Sapna On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: sapna sarupria wrote: Hi all, I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big box (~25 nm) in a box and find that the simulations are rather slow. I am getting about 0.8 ns per day when a simulation of bulk system of equivalent number of waters will be much faster. The number of waters is ~12000. I was wondering if anyone can suggest methods with which I can speed up the simulations. I am using domain decomposition and optimize_fft is set to yes. PME is used for the electrostatics. I would suspect that the lag comes from a lot of unused PME calculations. During your run, PME grid points will be assigned to vacuum space, for which nothing needs to be done. You can check imbalances and performance loss in the log file. -Justin Thank you Sincerely Sapna -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Speeding up simulation
Sapna, Is there a particular reason you're using a box so much larger than the droplet diameter? If your only concern is that periodic images should not see each-other maybe you can use a box length=droplet diameter+2*largest cut-off in the system. Also using a more spherical box shape such as rhombic dodecahedron or the truncated octahedron will help you in reducing the volume of unfilled space. -Gaurav On Tue, Aug 17, 2010 at 5:40 PM, sapna sarupria sapna.sarup...@gmail.comwrote: Hi Justin Thanks for your input. I guess I will do some more literature search and try to optimize the simulations as much as I can. Thanks, Sapna On Tue, Aug 17, 2010 at 5:36 PM, Justin A. Lemkul jalem...@vt.edu wrote: sapna sarupria wrote: Hi Justin Thanks for your response. I suspect that it is the same thing. Is there a way to make gromacs use PME only within a certain region of the simulation box? Also, how does one know how to fix the load imbalances (in this context)? There is no way to limit PME to certain ranges. It is a method for solving infinite sums. Usually PME is a poor choice for in vacuo simulations and the like, since there's nothing to be done for most of the simulation box. You may want to see how others (in the literature) deal with droplet-type simulations. -Justin Thanks for your help. Sapna On Tue, Aug 17, 2010 at 5:29 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: sapna sarupria wrote: Hi all, I am running (NVT) simulations of a drop of water (~5 nm in radius) in a big box (~25 nm) in a box and find that the simulations are rather slow. I am getting about 0.8 ns per day when a simulation of bulk system of equivalent number of waters will be much faster. The number of waters is ~12000. I was wondering if anyone can suggest methods with which I can speed up the simulations. I am using domain decomposition and optimize_fft is set to yes. PME is used for the electrostatics. I would suspect that the lag comes from a lot of unused PME calculations. During your run, PME grid points will be assigned to vacuum space, for which nothing needs to be done. You can check imbalances and performance loss in the log file. -Justin Thank you Sincerely Sapna -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sapna Sarupria Post-doctoral Researcher Princeton University New Jersey 08540 U.S.A. Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. Dare to Dream -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to
Re: [gmx-users] RE: log files
On Wed, Aug 11, 2010 at 1:10 PM, Nimesh Jain nimeshjain2...@u.northwestern.edu wrote: Well, no. I got a 20GB log file when nstlog was 1000. When I changed it to 1, the log file was about 1 MB after a few minutes of simulation which means that it will be in GBs in a few days. Did you re-compile using grompp after changing nstlog? Otherwise in md.tpr (output of grompp), nstlog=1000. -Gaurav On Wed, Aug 11, 2010 at 10:49 AM, Gaurav Goel gauravgoel...@gmail.comwrote: You've set the frequency of writing to log file as 'nstlog = 10'. Given that 'nsteps = 1', you're writing to the log file only 1000 times. Do you get a 20GB md.log file with these settings? -Gaurav On Wed, Aug 11, 2010 at 10:52 AM, Nimesh Jain nimeshjain2...@u.northwestern.edu wrote: Hi, I am having some problem in my simulations related to log files. The file sizes are enormous, its like after 3 days of simulation I had a 20 GB md.log file. One of my grompps looks like this: [tau_t is very low because I am using bd and it doesn't work otherwise]. [I am doing a replica exchange with 10,000 as exchange frequency] include = define = integrator = bd tinit= 0 dt = 0.001 nsteps = 1 ;10 simulation_part = 1 init_step= 0 comm-mode= Angular nstcomm = 1 comm-grps= emtol= 0.01 emstep = 1.5 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 10 nstenergy= 1000 nstxtcout= 1000 xtc-precision= 1000 xtc-grps = energygrps = ns_type = grid pbc = xyz periodic_molecules = no rlist= 8.95 coulombtype = user rcoulomb-switch = 0 rcoulomb = 8.95 epsilon-r= 1 vdw-type = user ;cutoff rvdw-switch = 0 rvdw = 8.95 DispCorr = No table-extension = 1 ; Seperate tables between energy group pairs energygrps = A T G C P260 SA SB energygrp_table = A A A T A G A C A P260 A SA A SB T T T G T C T P260 T S A T SB G G G C G P260 G SA G SB C C C P260 C SA C SB P260 P260 P260 SA P260 SB SA SA SA SB SB SB ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.10 Tcoupl = Nose-Hoover tc-grps = System tau_t= 0.0001 ref_t= 260.00 Pcoupl = No andersen_seed= 815131 gen_vel = yes gen_temp = 260. gen_seed = 1993 ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are excluded energygrp_excl = Please let me know if anyone knows whats the problem. Thanks, Nimesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Nimesh Jain Graduate Student Biomedical Engineering Northwestern University -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] RE: log files
You've set the frequency of writing to log file as 'nstlog = 10'. Given that 'nsteps = 1', you're writing to the log file only 1000 times. Do you get a 20GB md.log file with these settings? -Gaurav On Wed, Aug 11, 2010 at 10:52 AM, Nimesh Jain nimeshjain2...@u.northwestern.edu wrote: Hi, I am having some problem in my simulations related to log files. The file sizes are enormous, its like after 3 days of simulation I had a 20 GB md.log file. One of my grompps looks like this: [tau_t is very low because I am using bd and it doesn't work otherwise]. [I am doing a replica exchange with 10,000 as exchange frequency] include = define = integrator = bd tinit= 0 dt = 0.001 nsteps = 1 ;10 simulation_part = 1 init_step= 0 comm-mode= Angular nstcomm = 1 comm-grps= emtol= 0.01 emstep = 1.5 nstxout = 1 nstvout = 1 nstfout = 1 nstlog = 10 nstenergy= 1000 nstxtcout= 1000 xtc-precision= 1000 xtc-grps = energygrps = ns_type = grid pbc = xyz periodic_molecules = no rlist= 8.95 coulombtype = user rcoulomb-switch = 0 rcoulomb = 8.95 epsilon-r= 1 vdw-type = user ;cutoff rvdw-switch = 0 rvdw = 8.95 DispCorr = No table-extension = 1 ; Seperate tables between energy group pairs energygrps = A T G C P260 SA SB energygrp_table = A A A T A G A C A P260 A SA A SB T T T G T C T P260 T S A T SB G G G C G P260 G SA G SB C C C P260 C SA C SB P260 P260 P260 SA P260 SB SA SA SA SB SB SB ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.10 Tcoupl = Nose-Hoover tc-grps = System tau_t= 0.0001 ref_t= 260.00 Pcoupl = No andersen_seed= 815131 gen_vel = yes gen_temp = 260. gen_seed = 1993 ; ENERGY GROUP EXCLUSIONS ; Pairs of energy groups for which all non-bonded interactions are excluded energygrp_excl = Please let me know if anyone knows whats the problem. Thanks, Nimesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Reduced Units
On Mon, Aug 9, 2010 at 9:58 AM, poj...@icp.uni-stuttgart.de wrote: Hi, I want to use the pme algorithm in GROMACS. Thge size of my box is 8.2x8.2x8.2 in reduced units. I am considering a collection of 1000 of CO2 molecules. If I am using reduced units, the values of the parameters rcoulomb=0.9 I think should be converted to reduced units rcoulomb=2.45 (my \sigma=0.366nm). But my question is how can one convert the value of fourierspacing=0.12 to reduced units? 'fourierspacing' is also in units of length and it's value is used to determine 'fourier_nx' etc., if the latter are set to zero. In that case, fourier_nx=(box length along x)/fourierspacing. So for same level of PME accuracy scale down 'fourierspacing' by sigma=0.366 also. (This script is in SI standard units) ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = pme rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] does generating velocity keep centre of mass motion zero?
I'm doing NVE simulations so I've set comm_mode=None. Now my questions is regarding the generation of initial velocity with this- gen_vel = yes gen_temp= 4000 ; initial temperature gen_seed= 10234 The reason I do not want to use velocities from the end of my pre-equilibrated simulation (a NPT simulations followed by NVT simulation to get desired P,T) is to generate different trajectories by changing gen_seed. Does the generation of velocities above keep the centre of mass motion zero? It is important for me since comm_mode=None. Thanks, Gaurav -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] extracting coordinates
What do you want to do with the coordinates? Look-up 'trjconv' -Gaurav On Tue, Jul 20, 2010 at 11:32 AM, Vishal Agarwal vishal.iit...@gmail.comwrote: Dear All, I am new to using GROMACS. I have done some NVT simulation on glucose molecule. Can one anyone tell me how to extract the coordinates of atoms for each frame from the output trajectory file. Thanks, Vishal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_msd
On Mon, Jul 12, 2010 at 5:22 PM, Ricardo Cuya Guizado rcu...@hotmail.com wrote: Dear gromacs users I make a MD of 20 ns of a solute in water With the g_msd program the msd vs the time was obtained In the plot, I observed a linear behaviour of the MSD from 0 to 15 ns and a plateau with no linear tendence at the last 5 ns arpoximately. In order to know if the observed plateau was due to the data or is due to the way as the algorithm process the data, I divided the MD in two trajectories and obtained the msd for each one. From 0-10ns, the plot observed shows a linear tendence en the begining and a plateau with no linear tendence from 9 to 10 ns. From 10-20 ns the plot observed was linear from 10 to 18 ns and not linear at the last, the same plateau was observed. Comparing the plots there are not equivalent,. Why g_msd produces a non linear plot at the last of the calculation and the plateau is ever produces. Somebody will explain the way as the g_msd algorithm work? and why the plot are no equivalent or why there must be equivalent? I will explain how the g_msd algorithm works and hopefully that will answer all your questions above. What you see in the output file is average-MSD versus time. This average is done over all the particles in the group you selected and over multiple time origins (this last option can be selected with the -trestart parameter). Also, time in column 1 is time difference from the start of your trajectory to current time. E.g., let's say you collected a trajectory over 5 time units and choose -trestart=1 time unit and -dt=1 time unit. dt=1 means you'll have 6 configurations for your analysis (including the configuration at t=0). trestart=1 means you'll have 5 distinct trajectories for your analysis: Trajectory 1: 0-5 T2: 1-5 T3: 2-5 T4: 3-5 T5: 4-5 Now you can notice that all 5 trajectories contribute to the average MSD after 1 time unit (T1-T5), 4 trajectories contribute to the average MSD after 2 time units (T1-T4), 3 trajectories to the average MSD after 3 time units (T1-T3), , and only one trajectory to the MSD after 5 time units (T1). Of course, this assumes that trestart is large enough that all all these trajectories are uncorrelated. So, it's clear that longer the time interval at which you want to evaluate the MSD lesser the number of trajectories used to evaluate it...and hence, higher error in MSD values at longer times. That might explain deviation from linear behaviour at long times. However, you must be careful in interpreting the MSD data and I recommend reading some literature on the subject. A plateau in MSD versus time data might also signify what is called cage motion, in which a particle or atom is trapped by the surrounding particles and is not able to move out of that hole on the simulation time scale. If you want you can send me your MSD versus time data along with some information on your system (such as potentials, density, temperature etc.) and I can let you know my comments. Few words of caution: Make sure that the center of mass of your particle (or atom or molecule) is diffusing several particle diameters. Also, make sure that you're calculating the self-diffusion coefficient by fitting a straight line to the linear region of MSD versus time data. You can either modify the -beginfit and -endfit options... or calculate the slope of the MSD versus time data using some other software (e.g., gnuplot, excel, etc.). If you're doing the latter you'll need to take a look at the code in gmx_msd.c to know how the diffusion coefficent is calculated from the slope of MSD versus time data (tog et correct units, use proper scaling factors, etc.). I hope that helped. -Gaurav Regards Ricardo Cuya Courez la chance de voir la photo de votre coin de pays sur Bing.ca Soumettez une photo maintenant! -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with Lennard Jones cross terms
By specifying both c6 and c12 to be zero, you've set both the attractive and repulsive components of SI-OA, Si-CH2, Si-CH3 dispersion interactions to zero. If you don't have any electrostatic repulsions in your system polymer might be attracted to Silica substrate for entropic reasons...e.g., centers of mass of Si and CH2 can overlap without any energy penalty. One solution will be to fix c6, c12 for SI-OA, Si-CH2, Si-CH3 to their original values under *[ nonbond_params ] *and then do whatever you want to do with the Si-Si interactions in [atomtypes]. -Gaurav 2010/7/1 xrysostomos sfhsdfghsdfhsdgh cbat...@yahoo.gr I am trying to simulate the following system: 5-layer FCC substrate consisting of Si particles which interact only with Lennard-Jones potential and vertical to the substrate I put polymer chains of (CH2-OA), starting from a distance of 0,4nm. What I want is to be able to manage completely independently the LJ interactions between the substrate and the polymers and not according to the combination rules, i.e. to have very very strong LJ interaction only between the Si particles but these to interact normally with the polymer chains. I use the Gromos-96 force-field. The initial values for the c6 and c12 parameters are the following: *[ atomtypes ]* name at.num mass charge ptypec6 c12 OA 8 0.000 0.000 A 0.0022619536 1.505529e-06 CH26 0.000 0.000 A 0.0074684164 3.3965584e-05 SI140.000 0.000 A 0.01473796 2.2193521e-05 *[ nonbond_params ]* i j func c6 c12 SI OA 1 0.000 0. SI CH2 1 0.000 0. SI CH3 1 0.000 0. What I did is to run 2 different simulations in NVT ensemble. In the * first*, I multiplied by 10 the c6, c12 values of Si in the [atomtypes ] and in the *second* I multiplied (the initial values again) by 100. In both cases I didn’t change the values on the [nonbond_params ]. I would expect that in both cases there should be no adsorption of the polymers in the substrate, since I change the interaction between the substrate and the polymers in the [nonbond_params ] equal to zero. What I observed is that after 5 steps with 2 fs time step the polymers in the second case adsorbed to the surface. Can anybody help me or explain me why is this happening? Thanks in advance Chrysostomos -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with Lennard Jones cross terms
2010/7/1 xrysostomos sfhsdfghsdfhsdgh cbat...@yahoo.gr Dear Gaurav Thanks a lot for your quick reply I have done also what you suggested but the result is the same. I mean that I observe stronger adsorption of the polymers to the surface, when I increased the values of c6 and c12 for Si in the [atomtypes], but continue having original values in the *[ nonbond_params ].* But in general, am I not able with gromacs to switch-off the LJ interactions between the polymers and the substrate? Is it possible to have this problems because I use NVT ensemble? You can switch-off all non-bonded interactions between a pair of energy groups by defining Energy group exclusions. Sec. 7.3.19 of the gromacs manual 4.0. -Gaurav Thanks again, Chrysostomos --- Στις *Πέμ., 01/07/10, ο/η Gaurav Goel gauravgoel...@gmail.com*έγραψε: Από: Gaurav Goel gauravgoel...@gmail.com Θέμα: Re: [gmx-users] Problem with Lennard Jones cross terms Προς: Discussion list for GROMACS users gmx-users@gromacs.org Ημερομηνία: Πέμπτη, 1 Ιούλιος 2010, 16:10 By specifying both c6 and c12 to be zero, you've set both the attractive and repulsive components of SI-OA, Si-CH2, Si-CH3 dispersion interactions to zero. If you don't have any electrostatic repulsions in your system polymer might be attracted to Silica substrate for entropic reasons...e.g., centers of mass of Si and CH2 can overlap without any energy penalty. One solution will be to fix c6, c12 for SI-OA, Si-CH2, Si-CH3 to their original values under *[ nonbond_params ] *and then do whatever you want to do with the Si-Si interactions in [atomtypes]. -Gaurav 2010/7/1 xrysostomos sfhsdfghsdfhsdgh cbat...@yahoo.grhttp://mc/compose?to=cbat...@yahoo.gr I am trying to simulate the following system: 5-layer FCC substrate consisting of Si particles which interact only with Lennard-Jones potential and vertical to the substrate I put polymer chains of (CH2-OA), starting from a distance of 0,4nm. What I want is to be able to manage completely independently the LJ interactions between the substrate and the polymers and not according to the combination rules, i.e. to have very very strong LJ interaction only between the Si particles but these to interact normally with the polymer chains. I use the Gromos-96 force-field. The initial values for the c6 and c12 parameters are the following: *[ atomtypes ]* name at.num mass charge ptypec6 c12 OA 8 0.000 0.000 A 0.0022619536 1.505529e-06 CH26 0.000 0.000 A 0.0074684164 3.3965584e-05 SI140.000 0.000 A 0.01473796 2.2193521e-05 *[ nonbond_params ]* i j func c6 c12 SI OA 1 0.000 0. SI CH2 1 0.000 0. SI CH3 1 0.000 0. What I did is to run 2 different simulations in NVT ensemble. In the * first*, I multiplied by 10 the c6, c12 values of Si in the [atomtypes ] and in the *second* I multiplied (the initial values again) by 100. In both cases I didn’t change the values on the [nonbond_params ]. I would expect that in both cases there should be no adsorption of the polymers in the substrate, since I change the interaction between the substrate and the polymers in the [nonbond_params ] equal to zero. What I observed is that after 5 steps with 2 fs time step the polymers in the second case adsorbed to the surface. Can anybody help me or explain me why is this happening? Thanks in advance Chrysostomos -- gmx-users mailing list gmx-users@gromacs.orghttp://mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.orghttp://mc/compose?to=gmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/mailing_lists/users.php -Ακολουθεί συνημμένο- -- gmx-users mailing list gmx-users@gromacs.orghttp://mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.orghttp://mc/compose?to=gmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http
[gmx-users] Should I use separate PME nodes
I ran my simulation in parallel on 4 nodes (with zero separate PME nodes). Below is the information printed in md.log. I see that PME-Mesh calculations took 60% of CPU time. Any recommendations on using 1 or more separate PME nodes to speed up? Computing: M-Number M-Flops % Flops --- Coul(T) + VdW(T) 1761401.496982 119775301.79520.2 Outer nonbonded loop 106414.135764 1064141.358 0.2 Calc Weights 32400.006480 1166400.233 0.2 Spread Q Bspline 2332800.466560 4665600.933 0.8 Gather F Bspline 2332800.46656027993605.599 4.7 3D-FFT 47185929.437184 377487435.49763.6 Solve PME 675840.13516843253768.651 7.3 NS-Pairs 823453.92765617292532.481 2.9 Reset In Box2160.0021606480.006 0.0 CG-CoM 2160.0043206480.013 0.0 Virial 11700.002340 210600.042 0.0 Ext.ens. Update10800.002160 583200.117 0.1 Stop-CM10800.002160 108000.022 0.0 Calc-Ekin 10800.004320 291600.117 0.0 --- Total 593905146.863 100.0 --- R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Number G-CyclesSeconds % --- Domain decomp. 4101 3859.416 1488.1 0.6 Comm. coord. 4501 1874.635 722.8 0.3 Neighbor search410178640.72230322.211.2 Force 4501 180659.90269658.525.8 Wait + Comm. F 4501 2578.994 994.4 0.4 PME mesh 4501 422268.834 162817.760.4 Write traj.4 10001 17.5266.8 0.0 Update 4501 2981.794 1149.7 0.4 Comm. energies 4501 2633.176 1015.3 0.4 Rest 43580.341 1380.5 0.5 --- Total 4 699095.342 269556.0 100.0 --- Thanks, Gaurav -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] vdwtype=shift
section 7.3.11 of gromacs manual (v4.0)/ -Gaurav On Thu, Jun 24, 2010 at 4:40 AM, Erik Marklund er...@xray.bmc.uu.se wrote: you zou skrev: Dear users, I have a question about vdwtype. My question is if I use vdwtype=shift in nvt.mdp file: ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) ; Method for doing Van der Waals vdwtype = shift ; cut-off lengths rvdw-switch = 0 rvdw = 0.9, I have this error: Fatal error: With dispersion correction rvdw-switch can not be zero for vdw-type = Shift That I don't know how can I solve this problem. Thank you Hotmail: Powerful Free email with security by Microsoft. Get it now. https://signup.live.com/signup.aspx?id=60969 Errr... Setting rvdw-switch to a non-zero value might be worth trying. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 er...@xray.bmc.uu.se http://folding.bmc.uu.se/ -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem install gromacs in parallel
I'm trying to install a local copy of GROMACS on Ohio Super Computer. I was able to build single and double precision versions (did make distclean after each), however, got errors while installing parallel version. I will appreciate you taking time to help with this installation. Thanks. This is what I did: export CPPFLAGS=$FFTW_CFLAGS export LDFLAGS=$FFTW_LIBS contents of FFTW_CFLAGS=-I/usr/local/fftw3-3.1.2/include fftw3.f fftw3.h ***contents of FFTW_LIBS=-L/usr/local/fftw3-3.1.2/lib -lfftw3 -lfftw3f -lm libfftw3.alibfftw3f.solibfftw3.lalibfftw3.so.3.1.2 libfftw3f.a libfftw3f.so.3 libfftw3.sopkgconfig libfftw3f.la libfftw3f.so.3.1.2 libfftw3.so.3 ***output from './configure --enable-mpi --prefix=/nfs/18/cwr0350/my_gromacs/gromacs_1_bin --program-suffix=_mpi config.out' checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking for mpxlc... no checking for mpicc... mpicc checking whether the MPI cc command works... yes checking for catamount... no checking how to run the C preprocessor... mpicc -E checking whether mpicc accepts -O3... yes checking whether mpicc accepts -funroll-all-loops... no checking whether mpicc accepts -std=gnu99... no checking whether mpicc accepts -fast -pc 32 -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused... no *** * Sorry, these optimization settings don't seem to work for * * your C compiler. Use make CFLAGS=..., or edit the top Makefile. * *** checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether byte ordering is bigendian... no checking for int... yes checking size of int... 4 checking for long int... yes checking size of long int... 8 checking for long long int... yes checking size of long long int... 8 checking for off_t... yes checking size of off_t... 8 checking that size_t can hold pointers... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking for a BSD-compatible install... /usr/bin/install -c checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by mpicc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from mpicc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if mpicc supports -fno-rtti -fno-exceptions... no checking for mpicc option to produce PIC... -fPIC checking if mpicc PIC flag -fPIC works... yes checking if mpicc static flag -static works... no checking if mpicc supports -c -o file.o... yes checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... pgcc-Warning-Unknown switch: -print-search-dirs /usr/lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared
Re: [gmx-users] how small rcoulomb can be
Thanks for your reply Mark. On Wed, Jun 16, 2010 at 6:11 PM, Mark Abraham mark.abra...@anu.edu.au wrote: - Original Message - From: Gaurav Goel gauravgoel...@gmail.com Date: Thursday, June 17, 2010 5:21 Subject: [gmx-users] how small rcoulomb can be To: Discussion list for GROMACS users gmx-users@gromacs.org For my NPT/NVT simulations I'm using a BKS potential for dispersion interactions (VdWtype=USER) which has a cut-off of 0.55 nm. I also set rcoulomb=rlist=0.55 nm. My first question is regarding the choice of rcoulomb=0.55nm. Any thoughts on whether this rcoulomb is large enough to ascertain that real space electrostatics interactions are fairly small (in comparison to total coulombic interactions)? That's around half the size of typical rcoulomb values used for PME, so you'll need to adjust ewald_rtol and fourier_spacing to a considerable degree in order that the electrostatics your PME model is comparably accurate. If this model has been used with PME in the past, then you will have some guidance in its literature (though GROMACS does not make it easy to choose beta directly). This will mean the reciprocal-space processors are doing lots more work than normal, and you'll want to set -npme to be half of -np, or maybe zero. Even so, your parallel scaling will be noticeably worse than normal PME. Thanks for your reply Mark. Any thoughts on instead increasing rcoulomb and rlist. Will that be more efficient and/or accurate rather than trying to adjust ewald_rtol and fourier_spacing with a very short rcoulomb? In literature I found that the optimal value people have used for beta is, beta*L=10. In my simulations, for rcoulomb=0.55, beta*L=15.52 rcoulomb=0.9, beta*L= 9.49 How can I obtain the magnitude of maximum wave vector (i.e., 'm' in Eq. 4.159 of manual 4.0)? I have a separate question in regards to (conserved) energy drift in a NVT simulation. I first equilibrated my system for 1 ns in NPT ensemble. Then, I turned-off the pressure coupling, further equilibrated my system for 1 ns In NVT ensemble [N=2160, V=20.43 nm^3, T=4000K; rcoulomb=rlist=0.9, rvdw=0.55, nstlist=5]. Then in a production run of 3.5ns I get following energy drifts: Statistics over 3549897 steps [ 1000. thru 4549.8960 ps ], 1 data sets All averages are exact over 3549897 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Conserved En.-3.65264e+06 1893673.102718.4782 65595.7 i.e. drift=0.16 kT/ns. If nstlist=10, drift= 0.5kT/ns Should I worry about these drifts? -Gaurav Mark My second question is in regards to doing long (~15-100 ns) NVE simulations. It appears using coulombtype=PME-Switch will be the best option to accurately conserve energy. Any thoughts on how to choose rcoulomb_switch and rcoulomb? Thanks, Gaurav -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how small rcoulomb can be
I will re-ask my question as it didn't come out right in previous mail. Read below. On Wed, Jun 16, 2010 at 6:11 PM, Mark Abraham mark.abra...@anu.edu.au wrote: - Original Message - From: Gaurav Goel gauravgoel...@gmail.com Date: Thursday, June 17, 2010 5:21 Subject: [gmx-users] how small rcoulomb can be To: Discussion list for GROMACS users gmx-users@gromacs.org For my NPT/NVT simulations I'm using a BKS potential for dispersion interactions (VdWtype=USER) which has a cut-off of 0.55 nm. I also set rcoulomb=rlist=0.55 nm. My first question is regarding the choice of rcoulomb=0.55nm. Any thoughts on whether this rcoulomb is large enough to ascertain that real space electrostatics interactions are fairly small (in comparison to total coulombic interactions)? That's around half the size of typical rcoulomb values used for PME, so you'll need to adjust ewald_rtol and fourier_spacing to a considerable degree in order that the electrostatics your PME model is comparably accurate. If this model has been used with PME in the past, then you will have some guidance in its literature (though GROMACS does not make it easy to choose beta directly). This will mean the reciprocal-space processors are doing lots more work than normal, and you'll want to set -npme to be half of -np, or maybe zero. Even so, your parallel scaling will be noticeably worse than normal PME. Thanks for your reply Mark. Any thoughts on instead increasing rcoulomb and rlist. Will that be more efficient and/or accurate rather than trying to adjust ewald_rtol and fourier_spacing with a very short rcoulomb? In literature I found that the optimal value people have used for beta is, beta*L=10. In my simulations, for rcoulomb=0.55, beta*L=15.52 rcoulomb=0.9, beta*L= 9.49 How can I obtain the magnitude of maximum wave vector (i.e., 'm' in Eq. 4.159 of manual 4.0)? I have a separate question in regards to (conserved) energy drift in a NVT simulation. I first equilibrated my system for 1 ns in NPT ensemble. Then, I turned-off the pressure coupling, further equilibrated my system for 1 ns In NVT ensemble [N=2160, V=20.43 nm^3, T=4000K; rcoulomb=rlist=0.9, rvdw=0.55, nstlist=5]. Then in a production run of 3.5ns I get following energy drifts: Statistics over 3549897 steps [ 1000. thru 4549.8960 ps ], 1 data sets All averages are exact over 3549897 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Conserved En.-3.65264e+06 1893673.102718.4782 65595.7 i.e. drift=0.16 kT/ns. If nstlist=10, drift= 0.5kT/ns Should I worry about these drifts? -Gaurav Mark My second question is in regards to doing long (~15-100 ns) NVE simulations. It appears using coulombtype=PME-Switch will be the best option to accurately conserve energy. Any thoughts on how to choose rcoulomb_switch and rcoulomb? Thanks, Gaurav -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how small rcoulomb can be
For my NPT/NVT simulations I'm using a BKS potential for dispersion interactions (VdWtype=USER) which has a cut-off of 0.55 nm. I also set rcoulomb=rlist=0.55 nm. My first question is regarding the choice of rcoulomb=0.55nm. Any thoughts on whether this rcoulomb is large enough to ascertain that real space electrostatics interactions are fairly small (in comparison to total coulombic interactions)? My second question is in regards to doing long (~15-100 ns) NVE simulations. It appears using coulombtype=PME-Switch will be the best option to accurately conserve energy. Any thoughts on how to choose rcoulomb_switch and rcoulomb? Thanks, Gaurav -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] enegry minimisation
Can you try using g_rms to compare the difference between the structures before and after EM. -Gaurav On Thu, May 20, 2010 at 7:53 AM, Justin A. Lemkul jalem...@vt.edu wrote: sonali dhindwal wrote: Hello Gaurav, Thanks for your reply, I did position restrained enegry minimisation, and used following .mdp file for the same title = protein cpp = /usr/bin/cpp ; the c pre-processor define = -DPOSRE constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 1000 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 pbc = xyz I included define = -DPOSRE, for restraining the atom postion, I used posre.itp which was genertaed by pdb2gmx. Have I done it correctly, because after this also many of the beeta sheets have become short, forming loops. Well, you haven't properly defined position restraints. The default (produced by pdb2gmx) requires define = -DPOSRES not -DPOSRE. If you have for some reason modified the topology, then maybe your approach is correct, but otherwise your position restraints are not being applied. I also find it very curious that such substantial changes are taking place during a simple energy minimization. Are you sure the effects you are seeing are not simply due to the visualization software you are using guessing the incorrect secondary structure type? I have had that experience numerous times, especially in the case of beta-strands. DSSP tells me that, geometrically, I have beta-strands, but the visualization software renders coil structures. In any case, large structural deviations during EM suggest something fundamentally wrong with the model. Usually the changes in EM are small, since it is performed at 0 K. Only huge forces would cause any sort of structural change. I also want to ask what is the meaning of fx fy and fz : Force constants (kJ mol^-1 nm^-2) in the x, y, and z directions. ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 7 1 1000 1000 1000 8 1 1000 1000 1000 9 1 1000 1000 1000 11 1 1000 1000 1000 12 1 1000 1000 1000 15 1 1000 1000 1000 18 1 1000 1000 1000 19 1 1000 1000 1000 20 1 1000 1000 1000 21 1 1000 1000 1000 22 1 1000 1000 1000 23 1 1000 1000 1000 which is there in posre.itp file, and if these should have value of 1000 1000 1000 each ? These default values are typically quite sufficient to restrain the structure. -Justin Thanks in advance. -- Sonali Dhindwal --- On *Wed, 19/5/10, Gaurav Goel /gauravgoel...@gmail.com/* wrote: From: Gaurav Goel gauravgoel...@gmail.com Subject: Re: [gmx-users] enegry minimisation To: sonali dhindwal sonali11dhind...@yahoo.co.in Date: Wednesday, 19 May, 2010, 8:39 PM For position restraints you need to do the following: 1. define a name.itp file which looks like: ; In this topology include file, you will find position restraint ; entries for all the heavy atoms in your original pdb file. ; This means that all the protons which were added by pdb2gmx are ; not restrained. [ position_restraints ] ; atom type fx fy fz 1 1 1000 1000 1000 5 1 1000 1000 1000 6 1 1000 1000 1000 ... ... _ 1,5,6 etc. are the atom indices you want to restrain. section 4.3.1 in manual. 2. Add define = -Dname to your mdp file 3. Add following lines to your topology file ; Include Position restraint file #ifdef name #include name.itp #endif 4. compile and run. I'm sure you will find mroe information on position-restrain simulation on gmx-users archive. -Gaurav On Wed, May 19, 2010 at 10:26 AM, sonali dhindwal sonali11dhind...@yahoo.co.in /mc/compose?to=sonali11dhind...@yahoo.co.in wrote: Hello Gaurav, Can you please help me in suggesting where should I look for providing parameters to constrain the protein backbone and then do EM and then how to run a short MD simulation by constraining the protein backbone. Sorry to bother you, but as I am new to Gromacs, your help will be highly appreciable. Thanks in advance -- Sonali Dhindwal --- On *Wed, 19/5/10, Gaurav Goel /gauravgoel...@gmail.com /mc/compose?to=gauravgoel...@gmail.com/* wrote: From: Gaurav Goel gauravgoel
Re: [gmx-users] enegry minimisation
After adding water you can do energy minimization (EM) in two steps: 1. Constrain the protein backbone and do EM. 2. Now do EM on the full system. 3. Run a short MD simulation by constraining the protein backbone. The above three steps will help hydrate the protein molecule with minimal distortion of protein structure. 4. Now run a MD on full system. for details looks here: http://www.google.com/url?sa=tsource=webct=rescd=2ved=0CBcQFjABurl=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdfei=jOPzS8a3Lab2MdX1_aAOusg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymgsig2=bY3NqXHmruR7eSLVyAuCHQ -Gaurav On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal sonali11dhind...@yahoo.co.in wrote: Sorry, but I couldnt get your question, I have used this .mdp file for energy minimisation after addition of water and using GROMOS96 43a1 force field : title= drg_trp cpp = /lib/cpp ; location of cpp on SGI define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4] constraints = none integrator = steep dt = 0.002; ps ! nsteps = 2000 nstlist = 10 ns_type = grid rlist= 0.9 coulombtype = PME ; Use particle-mesh ewald rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 I hope it will help you to guide me further Thanks -- Sonali Dhindwal --- On *Wed, 19/5/10, Erik Marklund er...@xray.bmc.uu.se* wrote: From: Erik Marklund er...@xray.bmc.uu.se Subject: Re: [gmx-users] enegry minimisation To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, 19 May, 2010, 5:31 PM sonali dhindwal skrev: Hello All This question may sound trivial to many, but as i am new to this field, please help. I want to ask a question regarding my previous query of distortion of protein strucutre after molecular dynamcs simulation. I have noticed that after enegry minimisation using steepest decent algorithm, using emtol of 1000 kJ mol^-1 nm^-1 , large amount of distortion occurs. So is it necessary to do enegry minimisation step before MD, because this is my modeled protein, and i have already done energy minimisation using different program and after that I have done refinement also. Thanks and regards ^ -- Sonali Dhindwal So how has your system setup changed since your previous EM? Addition of water? Cutoffs? PME? -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.se http://mc/compose?to=er...@xray.bmc.uu.se http://folding.bmc.uu.se/ -- gmx-users mailing list gmx-users@gromacs.orghttp://mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.orghttp://mc/compose?to=gmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] enegry minimisation
On Wed, May 19, 2010 at 9:18 AM, Justin A. Lemkul jalem...@vt.edu wrote: Gaurav Goel wrote: After adding water you can do energy minimization (EM) in two steps: 1. Constrain the protein backbone and do EM. 2. Now do EM on the full system. 3. Run a short MD simulation by constraining the protein backbone. The above three steps will help hydrate the protein molecule with minimal distortion of protein structure. Such finesse may certainly be beneficial. Just for clarity, though, what you are referring to is the application of (position) restraints, not constraints. http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints Justin, thanks for clarifying. I was referring to position restraints. -Gaurav -Justin 4. Now run a MD on full system. for details looks here: http://www.google.com/url?sa=tsource=webct=rescd=2ved=0CBcQFjABurl=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdfei=jOPzS8a3Lab2MdX1_aAOusg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymgsig2=bY3NqXHmruR7eSLVyAuCHQ http://www.google.com/url?sa=tsource=webct=rescd=2ved=0CBcQFjABurl=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdfei=jOPzS8a3Lab2MdX1_aAOusg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymgsig2=bY3NqXHmruR7eSLVyAuCHQ -Gaurav On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal sonali11dhind...@yahoo.co.in mailto:sonali11dhind...@yahoo.co.in wrote: Sorry, but I couldnt get your question, I have used this .mdp file for energy minimisation after addition of water and using GROMOS96 43a1 force field : title = drg_trp cpp = /lib/cpp ; location of cpp on SGI define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4] constraints = none integrator = steep dt = 0.002 ; ps ! nsteps = 2000 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME ; Use particle-mesh ewald rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; ; Energy minimizing stuff ; emtol = 1000.0 emstep = 0.01 I hope it will help you to guide me further Thanks -- Sonali Dhindwal --- On *Wed, 19/5/10, Erik Marklund /er...@xray.bmc.uu.se mailto:er...@xray.bmc.uu.se/* wrote: From: Erik Marklund er...@xray.bmc.uu.se mailto:er...@xray.bmc.uu.se Subject: Re: [gmx-users] enegry minimisation To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Date: Wednesday, 19 May, 2010, 5:31 PM sonali dhindwal skrev: Hello All This question may sound trivial to many, but as i am new to this field, please help. I want to ask a question regarding my previous query of distortion of protein strucutre after molecular dynamcs simulation. I have noticed that after enegry minimisation using steepest decent algorithm, using emtol of 1000 kJ mol^-1 nm^-1 , large amount of distortion occurs. So is it necessary to do enegry minimisation step before MD, because this is my modeled protein, and i have already done energy minimisation using different program and after that I have done refinement also. Thanks and regards ^ -- Sonali Dhindwal So how has your system setup changed since your previous EM? Addition of water? Cutoffs? PME? -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 er...@xray.bmc.uu.se http://mc/compose?to=er...@xray.bmc.uu.se http://folding.bmc.uu.se/ -- gmx-users mailing list gmx-us...@gromacs.org http://mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org http://mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-us...@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list
[gmx-users] reading velocity in the g_msd routine
Hello gmx-users users :) I am modifying the 'g_msd' utility to be able to calculate viscosities using the corresponding Einstein relationship according to equation 3.14 in Helfand E., Physical Review, 119, 1, 1960. The equation is similar to the mean-square displacement equation for self-diffusion coefficient with the position vector 'r_i ' replaced by 'r_ix p_iy' where p_iy is the particle momenta in y-direction. So basically I need to be able to read both position and velocities from the trajectory. Presently, gmx_msd.c uses 'read_first_x' and 'read_next_x' to read the coordinates. Can you please comment on how I can modify this code to read the corresponding velocities? Any help is greatly appreciated. thanks, Gaurav -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
