[gmx-users] Defined number of molecule of water into box
Dear all, is it possible to put into a box a defined number of particle?in other word, i'd like put into my system eg. 100 molecule of water, I tried with: genbox -cp protein.gro -cs -nmol 100 -try 1 -o out.gro but it does not work.Can you help me? Thanks! Anna -- 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] Heat of vap
On 2011-04-04 01.32, Justin A. Lemkul wrote: Elisabeth wrote: Elisabeth wrote: Dear David, I followed your instructions and calculated Heat of vaporization of my alkane once with one molecule in gas phase (no cutoff) and once with equivalent number of molecules as in liquid phase as Justin suggested. Results are as follows: To get heat of vaporization, you shouldn't be simulating just a single molecule in the gas phase, it should be an equivalent number of molecules as you have in the liquid phase. Hello David and Justin, My explanation was not clear. Below is the results for liquid phase and for gas phase I tried two cases: one single molecule and the other time for equivalent number of molecules as in liquid phase and thats why results are very similar. ( However Justin says one single molecule is not correct. I think when cutoffs is set to zero only bonded terms are What is not correct is comparing the potential energy of a liquid system of many molecules with a gas phase of a single molecule. Whether or not that was something you did still is not entirely clear, but to be very clear, that's what I was saying is incorrect to do. DHvap is based on conversion of equivalent systems between liquid and gas. treated and even where there are many particles in gas phase to get This is incorrect. Cutoffs of zero mean that all nonbonded interactions are calculated, they are not truncated. energies per mole of molecules i.e g_energy -nmol XXX must be used so values should be colse to a single molecules case.. please correct me! Anyway results for gas phase are close and this is not the issue now). You shouldn't need -nmol for any of this. Simply take the potential energy of the two systems (with equivalent numbers of molecules) and apply the formula I gave you several emails ago. NOO 1 molecule in the gas phase - Epot(g) in your case 59.2 kJ/mol N molecules in the liquid phase - Epot(l) (since this is per mole you DO need the -nmol option) in you case 34.7 kJ/mol DHvap = Epot(g) + kBT - Epot(l) = 59.2+2.5-34.7 = 27 kJ/mol which is quite close to hexane (28.9 kJ/mol). -Justin Liquid phase: Energy Average Err.Est. RMSD Tot-Drift --- LJ (SR) -27.3083 0.01 0.296591 -0.0389173 (kJ/mol) Coulomb (SR) 6.00527 0.0074 0.122878 0.00576827 (kJ/mol) Coul. recip. 5.59559 0.0032 0.0557413 0.00316957 (kJ/mol) Potential *34.6779 * 0.025 1.03468 -0.11177 (kJ/mol) Total Energy 86.4044 0.026 1.44353 -0.112587 (kJ/mol) *one single molecule in gas phase* Energy Average Err.Est. RMSD Tot-Drift --- LJ (SR) -2.24473 0.073 1.292 0.342696 (kJ/mol) Coulomb (SR) 11.5723 0.55 2.17577 -2.33224 (kJ/mol) Potential * 59.244 * 0.94 10.9756 6.35631 (kJ/mol) Total Energy 106.647 1 15.4828 6.78792 (kJ/mol) *equivalent number of molecules as in liquid* ( large box 20 nm) Statistics over 101 steps [ 0. through 2000. ps ], 4 data sets All statistics are over 11 points Energy Average Err.Est. RMSD Tot-Drift --- LJ (SR) -2.16367 0.053 0.171542 0.374027 (kJ/mol) Coulomb (SR) 11.2894 0.23 0.49105 -1.44437 (kJ/mol) Potential * 63.2369 * 1.1 2.47211 7.69756 (kJ/mol) Total Energy 114.337 1.1 2.65547 7.72258 (kJ/mol) Since pbc is set to NO molecules leave the box and I dont know if this all right. I hope the difference is acceptable...! For pbc = no there is no box. 0- I am going to do the same calculation but for some polymers solvated in the alkane. For binary system do I need to look at nonboded terms? and then run a simulation for a single polymer in vacuum? Can you please provide me with a recipe for Delta Hvap of the solute in a solvent? The method for calculating heat of vaporization is not dependent upon the contents of the system; it is a fundamental thermodynamic definition. Heat of vaporization is not something that can be calculated from a solute in a solvent. You can calculate DHvap for a particular system, but not some subset of that system. Thanks Justin. I am interested in the energy required to vaporize the solute in a particular solvent not the whole DHvap of the mixture. do you think this can be achieved by calculating nonbonded energies between solute and solvent? ( defining energy groups ..) 1- If I want to look at nonboded interactions only, do I have to add Coul. recip. to [ LJ (SR) + Coulomb (SR) ] ? The PME-related terms contain both solute-solvent, solvent-solvent, and potentially solute-solute terms (depending on the size and nature of the solute), so trying to interpret this term in some pairwise fashion is an exercise in futility. What you mean is when one uses PME interaction energies between components can not be decomposed? So the energy groups I defined to extract nonbonded energies are not giving
[gmx-users] Defined number of molecule of water into box
I solved with genbox -cp conf.gro -cs -maxsol 100 -p topol.top -o out.gro Thanks! Anna-- 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] implicit water and a layer of explicit water molecule
Dear all, I got some question about the implicit solvent.1) In gromacs, is it possible simulate a protein in a layer of explicit water, and put this system (protein + SOL) into a big box and make the MD simulation with implicit solvent? How I have to set the md.mdp parameter (; IMPLICIT SOLVENT ALGORITHM) in this case?Do you know some tutorial about this method? 2) I'd like to put into my box a definied number of explicit number of molecule of water eg. 100, soI usedgenbox -cp conf.gro -cs -maxsol 100 -p topol.top -o out.gro but the water molecule is not in the random position in the box, but is in clustered conformation.Is it possible tell to genbox to put in a random way, in all space the defined number of molecule? 3) For that system (100 explicit solvent molecule + implicit solvent) I generated the topol.tpr using the following set up into the mdp file: ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = GBSA ;GENERALIZED BORN ELECTROSTATICS; ;Algorithm for calculating Born radii gb_algorithm = Still grompp do not give problem at all, but mdrun give problem:segmantation fault or Norm of force =nanI think that the problem is the use of explicit water molecule and the implcit water together. Can you help me? All the best Anna -- 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] implicit water and a layer of explicit water molecule
On 4/04/2011 6:11 PM, battis...@libero.it wrote: Dear all, I got some question about the implicit solvent. 1) In gromacs, is it possible simulate a protein in a layer of explicit water, and put this system (protein + SOL) into a big box and make the MD simulation with implicit solvent? How I have to set the md.mdp parameter (; IMPLICIT SOLVENT ALGORITHM) in this case? Do you know some tutorial about this method? It can't work as simply as that, because the waters on the edge will fly off into the implicit solvent region. People have tried various things - check out the literature. 2) I'd like to put into my box a definied number of explicit number of molecule of water eg. 100, so I used genbox -cp conf.gro -cs -maxsol 100 -p topol.top -o out.gro but the water molecule is not in the random position in the box, but is in clustered conformation. Is it possible tell to genbox to put in a random way, in all space the defined number of molecule? What do you actually want - a uniform gas of a given density? 3) For that system (100 explicit solvent molecule + implicit solvent) I generated the topol.tpr using the following set up into the mdp file: ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = GBSA ;GENERALIZED BORN ELECTROSTATICS; ;Algorithm for calculating Born radii gb_algorithm = Still grompp do not give problem at all, but mdrun give problem: segmantation fault or Norm of force =nan I think that the problem is the use of explicit water molecule and the implcit water together. Maybe. We haven't got enough information to know. 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
[gmx-users] Setting the C6 LJ term for OPLSA FF
Dear all I need to change sigma and epsilon for non-bonded parameters of the OPLSA FF. In particular I want to set the attractive part of the LJ potential to zero (C6=0). In doing this I have read the manual but unfortunately the reported explanation did not help me. To understand how it works in a reliable way, I followed the Berk suggestions available at http://lists.gromacs.org/pipermail/gmx-users/2010-December/056303.html and i decided to report a simple example. The main rules are in forcefield.itp file and for OPLSA FF they are: ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.50.5 The non-bonded force field parameters for two atoms are in ffnonbonded.itp file and they look like: [ atomtypes ] ; name bond_type mass charge ptypesigma epsilon opls_1 C 612.01100 0.500A sig_1esp_1 opls_2 O 8 15.99940 -0.500 A sig_2eps_2 From these values I am going to define the non-bonded parameter between a couple of atoms as: [ nonbond_params ] i j func SIG_ij EPS_ij opls_1 opls_2 1(sig_1*sig2)^1/2 (eps_1*eps_2)^1/2 ; Normal behavior However, if I want the attractive term C6 of LJ potential equal zero, I should set sig_12=-sig_12 [ nonbond_params ] i j funcSIG_ij EPS_ij opls_1 opls_2 1 -(sig_1*sig_2)^1/2 (eps_1*eps_2)^1/2 ; -sig_ij - C6=0 It is right? Thanks Luca -- 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] Setting the C6 LJ term for OPLSA FF
On 4/04/2011 6:55 PM, Luca Bellucci wrote: Dear all I need to change sigma and epsilon for non-bonded parameters of the OPLSA FF. In particular I want to set the attractive part of the LJ potential to zero (C6=0). In doing this I have read the manual but unfortunately the reported explanation did not help me. To understand how it works in a reliable way, I followed the Berk suggestions available at http://lists.gromacs.org/pipermail/gmx-users/2010-December/056303.html and i decided to report a simple example. The main rules are in forcefield.itp file and for OPLSA FF they are: ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.50.5 The non-bonded force field parameters for two atoms are in ffnonbonded.itp file and they look like: [ atomtypes ] ; name bond_type mass charge ptypesigma epsilon opls_1 C 612.01100 0.500A sig_1esp_1 opls_2 O 8 15.99940 -0.500 A sig_2eps_2 From these values I am going to define the non-bonded parameter between a couple of atoms as: [ nonbond_params ] i j func SIG_ij EPS_ij opls_1 opls_2 1(sig_1*sig2)^1/2 (eps_1*eps_2)^1/2 ; Normal behavior However, if I want the attractive term C6 of LJ potential equal zero, I should set sig_12=-sig_12 [ nonbond_params ] i j funcSIG_ij EPS_ij opls_1 opls_2 1 -(sig_1*sig_2)^1/2 (eps_1*eps_2)^1/2 ; -sig_ij - C6=0 It is right? Yes, I think so. Set up a two-atom example to compare the normal and modified functions. Get a trajectory frame, make energy group(s) containing only pair(s) of atoms of interest and use mdrun -rerun to compute the energy to your heart's content. 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
R: [gmx-users] implicit water and a layer of explicit water molecule
Dear Mark, about point 2, yes I need to have a uniform distribution of a defined numberof water molecule (eg. 100 water molecule ) into my box. Is it possible with genbox? After, I'll have to make the md simulation for my system in implicit solvent (I'll have protein + 100 molecule SOL + implicit solvent) So my next problem is to set the parameter into mdp file, for this mixed type of kind of water. Thanks for your reply Anna Dear all, I got some question about the implicit solvent. 1) In gromacs, is it possible simulate a protein in a layer of explicit water, and put this system (protein + SOL) into a big box and make the MD simulation with implicit solvent? How I have to set the md.mdp parameter (; IMPLICIT SOLVENT ALGORITHM) in this case? Do you know some tutorial about this method? It can't work as simply as that, because the waters on the edge will fly off into the implicit solvent region. People have tried various things - check out the literature. 2) I'd like to put into my box a definied number of explicit number of molecule of water eg. 100, so I used genbox -cp conf.gro -cs -maxsol 100 -p topol.top -o out.gro but the water molecule is not in the random position in the box, but is in clustered conformation. Is it possible tell to genbox to put in a random way, in all space the defined number of molecule? What do you actually want - a uniform gas of a given density? 3) For that system (100 explicit solvent molecule + implicit solvent) I generated the topol.tpr using the following set up into the mdp file: ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = GBSA ;GENERALIZED BORN ELECTROSTATICS; ;Algorithm for calculating Born radii gb_algorithm = Still grompp do not give problem at all, but mdrun give problem: segmantation fault or Norm of force =nan I think that the problem is the use of explicit water molecule and the implcit water together. Maybe. We haven't got enough information to know. 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: R: [gmx-users] implicit water and a layer of explicit water molecule
On 4/04/2011 7:12 PM, battis...@libero.it wrote: Dear Mark, about point 2, yes I need to have a uniform distribution of a defined number of water molecule (eg. 100 water molecule ) into my box. Is it possible with genbox? Yes, but not by starting with a uniform distribution of a condensed-phase density. You need one of the right density to start with. A better approach is to decide how large a box of what density you want. Work out how much volume that gives to each molecule. Take a single molecule and put it in a box of that size with editconf. Move the molecule a bit off-center. Then use genconf -rot to replicate that box into a large one. Then equilibrate that thoroughly to get rid of the residual ordering. If, later on, you want a different size, genbox with the box you've equilibrated here will be a good approach. After, I'll have to make the md simulation for my system in implicit solvent (I'll have protein + 100 molecule SOL + implicit solvent) So my next problem is to set the parameter into mdp file, for this mixed type of kind of water. You have more problems than that. The force fields probably don't have implicit solvation parameters for water atom types. You'll need to source them somehow. And like I told you last time, your solvent molecules are not going to stay happily around your solvent like you hope. I'm going to stop repeating myself :-) 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
[gmx-users] FEP and loss of performance
Dear all, when I run a single free energy simulation i noticed that there is a loss of performace with respect to the normal MD free_energy= yes init_lambda= 0.9 delta_lambda = 0.0 couple-moltype = Protein_Chain_P couple-lambda0 = vdw-q couple-lambda0 = none couple-intramol= yes Average load imbalance: 16.3 % Part of the total run time spent waiting due to load imbalance: 12.2 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X0 % Time: 1852.712 1852.712100.0 free_energy= no Average load imbalance: 2.7 % Part of the total run time spent waiting due to load imbalance: 1.7 % Time:127.394127.394100.0 It seems that the loss of performace is due in part to in the load imbalance in the domain decomposition, however I tried to change these keywords without benefit Any comment is welcome. 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/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
R: [gmx-users] implicit water and a layer of explicit water molecule
Thank you very much for your suggestions! Anna -- 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] Check out my photos on Facebook
Hi Gmx-users, I set up a Facebook profile where I can post my pictures, videos and events and I want to add you as a friend so you can see it. First, you need to join Facebook! Once you join, you can also create your own profile. Thanks, Gokul To sign up for Facebook, follow the link below: http://www.facebook.com/p.php?i=12233939090k=Z6E3Y3UXVW4N6KDJPB63QUXV2W1GVX5NUV1PJBTGYQr Already have an account? Add this email address to your account: http://www.facebook.com/n/?merge_accounts.phpe=gmx-users%40gromacs.orgc=f3a89fc32e182e6abbd64f366ef3f589 === gmx-users@gromacs.org was invited to join Facebook by Gokul Algates. If you don't want to receive these emails from Facebook in the future, please follow the link below to unsubscribe. http://www.facebook.com/o.php?k=7c1955u=11958234951mid=403935cG5af385328b47G0G8 Learn more about this email: http://www.facebook.com/help/?faq=17151\nFacebook, Inc. P.O. Box 10005, Palo Alto, CA 94303 -- 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] Check out my photos on Facebook
Hi Gmx-users, I set up a Facebook profile where I can post my pictures, videos and events and I want to add you as a friend so you can see it. First, you need to join Facebook! Once you join, you can also create your own profile. Thanks, Gokul To sign up for Facebook, follow the link below: http://www.facebook.com/p.php?i=12233939090k=Z6E3Y3UXVW4N6KDJPB63QUXV2W1GVX5NUV1PJBUCU2r Already have an account? Add this email address to your account: http://www.facebook.com/n/?merge_accounts.phpe=gmx-users%40gromacs.orgc=f3a89fc32e182e6abbd64f366ef3f589 === gmx-users@gromacs.org was invited to join Facebook by Gokul Algates. If you don't want to receive these emails from Facebook in the future, please follow the link below to unsubscribe. http://www.facebook.com/o.php?k=7c1955u=11958234951mid=40390ecG5af385328b47G0G8 Learn more about this email: http://www.facebook.com/help/?faq=17151\nFacebook, Inc. P.O. Box 10005, Palo Alto, CA 94303 -- 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] Umbrella Sampling
Hi I assume that the order of the file names in the tpr-files.dat and pullx-files.dat is irrelevant for g_wham . Cheers Gavin -- 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] Umbrella Sampling
From g_wham -h: The tpr and pullx files must be in corresponding order, i.e. the first tpr created the first pullx, etc. -Justin Gavin Melaugh wrote: Hi I assume that the order of the file names in the tpr-files.dat and pullx-files.dat is irrelevant for g_wham . Cheers Gavin -- 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/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] minimization and simulation problems
Dear all,
I'm trying to run simulation of 30 proteins in water using the Martini
force field. I used water.gro file in order to solvate the proteins.
For minimization I used the em.mdp file published at Martini site
(http://md.chem.rug.nl/cgmartini/index.php/home). When I set the emtol
parameter to 10 the system can't converge. So I used emtol 100 and
then the system converged. I use it as an input for the simulation.
The file can't be attached as it is too big nut I can send it if needed.
However, the sumulation crushes when I'm trying to run MD using md.mdp
also from the Martini site. I'm getting the following warnings and
errors:
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
---
It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 8
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0[cli_0]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
---
Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 1 out of 8
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3[cli_3]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5[cli_5]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4[cli_4]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6[cli_6]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2[cli_2]:
aborting job:
application called
[gmx-users] FEP and loss of performance
If we accept your text at face value, then the simulation slowed down by a factor of 1500%, certainly not the 16% of the load balancing. Please let us know what version of gromacs and cut and paste your cammands that you used to run gromacs (so we can verify that you ran on the same number of processors) and cut and paste a diff of the .mdp files (so that we can verify that you ran for the same number of steps). You might be correct about the slowdown, but let's rule out some other more obvious problems first. Chris. -- original message -- Dear all, when I run a single free energy simulation i noticed that there is a loss of performace with respect to the normal MD free_energy= yes init_lambda= 0.9 delta_lambda = 0.0 couple-moltype = Protein_Chain_P couple-lambda0 = vdw-q couple-lambda0 = none couple-intramol= yes Average load imbalance: 16.3 % Part of the total run time spent waiting due to load imbalance: 12.2 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X0 % Time: 1852.712 1852.712100.0 free_energy= no Average load imbalance: 2.7 % Part of the total run time spent waiting due to load imbalance: 1.7 % Time:127.394127.394100.0 It seems that the loss of performace is due in part to in the load imbalance in the domain decomposition, however I tried to change these keywords without benefit Any comment is welcome. 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/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] minimization and simulation problems
What are your initial box dimensions prior to em? Also, please copy
and paste your .mdp options. Also, what happens when you run the same
post-em simulation with nsteps=1 ?
-- original message --
Dear all,
I'm trying to run simulation of 30 proteins in water using the Martini
force field. I used water.gro file in order to solvate the proteins.
For minimization I used the em.mdp file published at Martini site
(http://md.chem.rug.nl/cgmartini/index.php/home). When I set the emtol
parameter to 10 the system can't converge. So I used emtol 100 and
then the system converged. I use it as an input for the simulation.
The file can't be attached as it is too big nut I can send it if needed.
However, the sumulation crushes when I'm trying to run MD using md.mdp
also from the Martini site. I'm getting the following warnings and
errors:
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
---
It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 8
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0[cli_0]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
---
Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 1 out of 8
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3[cli_3]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5[cli_5]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4[cli_4]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6[cli_6]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process
Re: [gmx-users] Umbrella Sampling
Hi Justin Yeah I know the tpr files must be in corresponding order with pullx.xvg files. What I meant was should they be in order of distance. i.e say If my windows go from 0 to 1.0 nm with windows every 0.1nm, could I list the files in any order or does it have to like 0.1 0.2 0.3 0.4 Gavin Justin A. Lemkul wrote: From g_wham -h: The tpr and pullx files must be in corresponding order, i.e. the first tpr created the first pullx, etc. -Justin Gavin Melaugh wrote: Hi I assume that the order of the file names in the tpr-files.dat and pullx-files.dat is irrelevant for g_wham . Cheers Gavin -- 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] Umbrella Sampling
Gavin Melaugh wrote: Hi Justin Yeah I know the tpr files must be in corresponding order with pullx.xvg files. What I meant was should they be in order of distance. i.e say If my windows go from 0 to 1.0 nm with windows every 0.1nm, could I list the files in any order or does it have to like 0.1 0.2 0.3 0.4 As long as the order (in terms of matching) is correct, you shouldn't have a problem. You can easily test this by switching the position of just one pair of .tpr/.xvg files and seeing if you get the same result. -Justin Gavin Justin A. Lemkul wrote: From g_wham -h: The tpr and pullx files must be in corresponding order, i.e. the first tpr created the first pullx, etc. -Justin Gavin Melaugh wrote: Hi I assume that the order of the file names in the tpr-files.dat and pullx-files.dat is irrelevant for g_wham . Cheers Gavin -- 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/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] minimization and simulation problems
my box dimensions are 368A
Quoting chris.ne...@utoronto.ca:
What are your initial box dimensions prior to em? Also, please copy
and paste your .mdp options. Also, what happens when you run the
same post-em simulation with nsteps=1 ?
-- original message --
Dear all,
I'm trying to run simulation of 30 proteins in water using the Martini
force field. I used water.gro file in order to solvate the proteins.
For minimization I used the em.mdp file published at Martini site
(http://md.chem.rug.nl/cgmartini/index.php/home). When I set the emtol
parameter to 10 the system can't converge. So I used emtol 100 and
then the system converged. I use it as an input for the simulation.
The file can't be attached as it is too big nut I can send it if needed.
However, the sumulation crushes when I'm trying to run MD using md.mdp
also from the Martini site. I'm getting the following warnings and
errors:
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
---
It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 8
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0[cli_0]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
---
Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 1 out of 8
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3[cli_3]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5[cli_5]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4[cli_4]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6[cli_6]:
aborting
Re: [gmx-users] FEP and loss of performance
Hi Chris, thank for the suggestions, in the previous mail there is a mistake because couple-moltype = SOL (for solvent) and not Protein_chaim_P. Now the problem of the load balance seems reasonable, because the water box is large ~9.0 nm. However the problem exist and the performance loss is very high, so I have redone calculations with this command: grompp -f md.mdp -c ../Run-02/confout.gro -t ../Run-02/state.cpt -p ../topo.top -n ../index.ndx -o md.tpr -maxwarn 1 mdrun -s md.tpr -o md this is part of the md.mdp file: ; Run parameters ; define = -DPOSRES integrator = md; nsteps = 1000 ; dt = 0.002 ; [..] free_energy= yes ; /no init_lambda= 0.9 delta_lambda = 0.0 couple-moltype = SOL; solvent water couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol= yes Result for free energy calculation Computing: Nodes Number G-CyclesSeconds % --- Domain decomp. 8126 22.0508.3 0.1 DD comm. load 8 150.0090.0 0.0 DD comm. bounds 8 120.0310.0 0.0 Comm. coord.8 1001 17.3196.5 0.0 Neighbor search8127 436.569 163.7 1.1 Force 8 100134241.57612840.987.8 Wait + Comm. F8 1001 19.4867.3 0.0 PME mesh 8 1001 4190.758 1571.610.7 Write traj. 8 71.8270.7 0.0 Update 8 1001 12.5574.7 0.0 Constraints 8 1001 26.4969.9 0.1 Comm. energies 8 1002 10.7104.0 0.0 Rest 8 25.1429.4 0.1 --- Total 8 39004.53114627.1 100.0 --- --- PME redist. X/F 8 3003 3479.771 1304.9 8.9 PME spread/gather 8 4004 277.574 104.1 0.7 PME 3D-FFT 8 4004 378.090 141.8 1.0 PME solve 8 2002 55.033 20.6 0.1 --- Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 1828.385 1828.385100.0 30:28 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 3.115 3.223 0.095253.689 I Switched off only the free_energy keyword and I redone the calculation I have: Computing: Nodes Number G-CyclesSeconds % --- Domain decomp. 8 77 10.9754.1 0.6 DD comm. load 8 10.0010.0 0.0 Comm. coord. 8 1001 14.4805.4 0.8 Neighbor search 8 78 136.479 51.2 7.3 Force 8 1001 1141.115 427.961.3 Wait + Comm. F 8 1001 17.8456.7 1.0 PME mesh8 1001 484.581 181.726.0 Write traj. 8 51.2210.5 0.1 Update 8 10019.9763.7 0.5 Constraints8 1001 20.2757.6 1.1 Comm. energies 89925.9332.2 0.3 Rest 8 19.6707.4 1.1 --- Total 81862.552 698.5 100.0 --- --- PME redist. X/F8 2002 92.204 34.6 5.0 PME spread/gather 8 2002 192.337 72.110.3 PME 3D-FFT 8 2002 177.373 66.5 9.5 PME solve 8 1001 22.5128.4 1.2 --- Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 87.309 87.309100.0 1:27 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:439.731 23.995 1.981 12.114 Finished mdrun on node 0 Mon Apr 4 16:52:04 2011 Luca If we accept your text at face value, then the simulation
Re: [gmx-users] FEP and loss of performance
Luca Bellucci wrote: Hi Chris, thank for the suggestions, in the previous mail there is a mistake because couple-moltype = SOL (for solvent) and not Protein_chaim_P. Now the problem of the load balance seems reasonable, because the water box is large ~9.0 nm. Now your outcome makes a lot more sense. You're decoupling all of the solvent? I don't see how that is going to be physically stable or terribly meaningful, but it explains your performance loss. You're annihilating a significant number of interactions (probably the vast majority of all the nonbonded interactions in the system), which I would expect would cause continuous load balancing issues. -Justin However the problem exist and the performance loss is very high, so I have redone calculations with this command: grompp -f md.mdp -c ../Run-02/confout.gro -t ../Run-02/state.cpt -p ../topo.top -n ../index.ndx -o md.tpr -maxwarn 1 mdrun -s md.tpr -o md this is part of the md.mdp file: ; Run parameters ; define = -DPOSRES integrator = md ; nsteps = 1000 ; dt = 0.002 ; [..] free_energy= yes ; /no init_lambda= 0.9 delta_lambda = 0.0 couple-moltype = SOL; solvent water couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol= yes Result for free energy calculation Computing: Nodes Number G-CyclesSeconds % --- Domain decomp. 8126 22.0508.3 0.1 DD comm. load 8 150.0090.0 0.0 DD comm. bounds 8 120.0310.0 0.0 Comm. coord.8 1001 17.3196.5 0.0 Neighbor search8127 436.569 163.7 1.1 Force 8 100134241.57612840.987.8 Wait + Comm. F8 1001 19.4867.3 0.0 PME mesh 8 1001 4190.758 1571.610.7 Write traj. 8 71.8270.7 0.0 Update 8 1001 12.5574.7 0.0 Constraints 8 1001 26.4969.9 0.1 Comm. energies 8 1002 10.7104.0 0.0 Rest 8 25.1429.4 0.1 --- Total 8 39004.53114627.1 100.0 --- --- PME redist. X/F 8 3003 3479.771 1304.9 8.9 PME spread/gather 8 4004 277.574 104.1 0.7 PME 3D-FFT 8 4004 378.090 141.8 1.0 PME solve 8 2002 55.033 20.6 0.1 --- Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 1828.385 1828.385100.0 30:28 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance: 3.115 3.223 0.095253.689 I Switched off only the free_energy keyword and I redone the calculation I have: Computing: Nodes Number G-CyclesSeconds % --- Domain decomp. 8 77 10.9754.1 0.6 DD comm. load 8 10.0010.0 0.0 Comm. coord. 8 1001 14.4805.4 0.8 Neighbor search 8 78 136.479 51.2 7.3 Force 8 1001 1141.115 427.961.3 Wait + Comm. F 8 1001 17.8456.7 1.0 PME mesh8 1001 484.581 181.726.0 Write traj. 8 51.2210.5 0.1 Update 8 10019.9763.7 0.5 Constraints8 1001 20.2757.6 1.1 Comm. energies 89925.9332.2 0.3 Rest 8 19.6707.4 1.1 --- Total 81862.552 698.5 100.0 --- --- PME redist. X/F8 2002 92.204 34.6 5.0 PME spread/gather 8 2002 192.337 72.110.3 PME 3D-FFT 8 2002 177.373 66.5 9.5 PME solve 8 1001 22.5128.4 1.2 ---
[gmx-users] FEP and loss of performance
Load balancing problems I can understand, but why would it take longer in absolute time? I would have thought that some nodes would simple be sitting idle, but this should not cause an increase in the overall simulation time (15x at that!). There must be some extra communication? I agree with Justin that this seems like a strange thing to do, but still I think that there must be some underlying coding issue (probably one that only exists because of a reasonable assumption that nobody would annihilate the largest part of their system). Chris. Luca Bellucci wrote: / Hi Chris, // thank for the suggestions, // in the previous mail there is a mistake because // couple-moltype = SOL (for solvent) and not Protein_chaim_P. // Now the problem of the load balance seems reasonable, because // the water box is large ~9.0 nm. / Now your outcome makes a lot more sense. You're decoupling all of the solvent? I don't see how that is going to be physically stable or terribly meaningful, but it explains your performance loss. You're annihilating a significant number of interactions (probably the vast majority of all the nonbonded interactions in the system), which I would expect would cause continuous load balancing issues. -Justin / However the problem exist and the performance loss is very high, so I have // redone calculations with this command: // // grompp -f // md.mdp -c ../Run-02/confout.gro -t ../Run-02/state.cpt -p ../topo.top -n ../index.ndx -o // md.tpr -maxwarn 1 // // mdrun -s md.tpr -o md // // this is part of the md.mdp file: // // ; Run parameters // ; define = -DPOSRES // integrator = md; // nsteps = 1000 ; // dt = 0.002 ; // [..] // free_energy= yes ; /no // init_lambda= 0.9 // delta_lambda = 0.0 // couple-moltype = SOL; solvent water // couple-lambda0 = vdw-q // couple-lambda1 = none // couple-intramol= yes // // Result for free energy calculation // Computing: Nodes Number G-CyclesSeconds % // --- // Domain decomp. 8126 22.0508.3 0.1 // DD comm. load 8 150.0090.0 0.0 // DD comm. bounds 8 120.0310.0 0.0 // Comm. coord.8 1001 17.3196.5 0.0 // Neighbor search8127 436.569 163.7 1.1 // Force 8 100134241.57612840.9 87.8 // Wait + Comm. F8 1001 19.4867.3 0.0 // PME mesh 8 1001 4190.758 1571.610.7 // Write traj. 8 71.8270.7 0.0 // Update 8 1001 12.5574.7 0.0 // Constraints 8 1001 26.4969.9 0.1 // Comm. energies 8 1002 10.7104.0 0.0 // Rest 8 25.1429.4 0.1 // --- // Total 8 39004.53114627.1 100.0 // --- // --- // PME redist. X/F 8 3003 3479.771 1304.9 8.9 // PME spread/gather 8 4004 277.574 104.1 0.7 // PME 3D-FFT 8 4004 378.090 141.8 1.0 // PME solve 8 2002 55.033 20.6 0.1 // --- // Parallel run - timing based on wallclock. // // NODE (s) Real (s) (%) // Time: 1828.385 1828.385100.0 // 30:28 // (Mnbf/s) (GFlops) (ns/day) (hour/ns) // Performance: 3.115 3.223 0.095253.689 // // I Switched off only the free_energy keyword and I redone the calculation // I have: // Computing: Nodes Number G-CyclesSeconds % // --- // Domain decomp. 8 77 10.9754.1 0.6 // DD comm. load 8 10.0010.0 0.0 // Comm. coord. 8 1001 14.4805.4 0.8 // Neighbor search 8 78 136.479 51.2 7.3 // Force 8 1001 1141.115 427.961.3 // Wait + Comm. F 8 1001 17.8456.7 1.0 // PME mesh8 1001 484.581 181.726.0 // Write traj. 8 51.2210.5 0.1 // Update 8 1001
Re: [gmx-users] FEP and loss of performance
Dear Chris and Justin Thank you for your precious suggestions This is a test that i perform in a single machine with 8 cores and gromacs 4.5.4. I am trying to enhance the sampling of a protein using the decoupling scheme of the free energy module of gromacs. However when i decouple only the protein, the protein collapsed. Because i simulated in NVT i thought that this was an effect of the solvent. I was trying to decouple also the solvent to understand the system behavior. I expected a loss of performance, but not so drastic. Luca Load balancing problems I can understand, but why would it take longer in absolute time? I would have thought that some nodes would simple be sitting idle, but this should not cause an increase in the overall simulation time (15x at that!). There must be some extra communication? I agree with Justin that this seems like a strange thing to do, but still I think that there must be some underlying coding issue (probably one that only exists because of a reasonable assumption that nobody would annihilate the largest part of their system). Chris. Luca Bellucci wrote: / Hi Chris, // thank for the suggestions, // in the previous mail there is a mistake because // couple-moltype = SOL (for solvent) and not Protein_chaim_P. // Now the problem of the load balance seems reasonable, because // the water box is large ~9.0 nm. / Now your outcome makes a lot more sense. You're decoupling all of the solvent? I don't see how that is going to be physically stable or terribly meaningful, but it explains your performance loss. You're annihilating a significant number of interactions (probably the vast majority of all the nonbonded interactions in the system), which I would expect would cause continuous load balancing issues. -Justin / However the problem exist and the performance loss is very high, so I have // redone calculations with this command: // // grompp -f // md.mdp -c ../Run-02/confout.gro -t ../Run-02/state.cpt -p ../topo.top -n ../index.ndx -o // md.tpr -maxwarn 1 // // mdrun -s md.tpr -o md // // this is part of the md.mdp file: // // ; Run parameters // ; define = -DPOSRES // integrator = md; // nsteps = 1000 ; // dt = 0.002 ; // [..] // free_energy= yes ; /no // init_lambda= 0.9 // delta_lambda = 0.0 // couple-moltype = SOL; solvent water // couple-lambda0 = vdw-q // couple-lambda1 = none // couple-intramol= yes // // Result for free energy calculation // Computing: Nodes Number G-CyclesSeconds % // --- // Domain decomp. 8126 22.0508.3 0.1 // DD comm. load 8 150.0090.0 0.0 // DD comm. bounds 8 120.0310.0 0.0 // Comm. coord.8 1001 17.3196.5 0.0 // Neighbor search8127 436.569 163.7 1.1 // Force 8 100134241.57612840.9 87.8 // Wait + Comm. F8 1001 19.4867.3 0.0 // PME mesh 8 1001 4190.758 1571.6 10.7 // Write traj. 8 71.827 0.7 0.0 // Update 8 1001 12.557 4.7 0.0 // Constraints 8 1001 26.496 9.9 0.1 // Comm. energies 8 1002 10.710 4.0 0.0 // Rest 8 25.142 9.4 0.1 // --- // Total 8 39004.53114627.1 100.0 // --- // --- // PME redist. X/F 8 3003 3479.771 1304.9 8.9 // PME spread/gather 8 4004 277.574 104.1 0.7 // PME 3D-FFT 8 4004 378.090 141.8 1.0 // PME solve 8 2002 55.033 20.6 0.1 // --- // Parallel run - timing based on wallclock. // // NODE (s) Real (s) (%) // Time: 1828.385 1828.385100.0 // 30:28 // (Mnbf/s) (GFlops) (ns/day) (hour/ns) // Performance: 3.115 3.223 0.095253.689 // // I Switched off only the free_energy keyword and I redone the calculation // I have: // Computing: Nodes Number G-CyclesSeconds % // --- //
[gmx-users] g_mdmat distance matrices
Dear gmx users, I used g_mdmat and have got a distance matrices in .xpm format. Now I want to compare two matrices: for a protein var1 and for protein var2 and create one output file with this compare. How can I do it? If there is no such function in gromacs, how can I convert .xpm format to get a matrices with numbers? -- Sincerely, Yulian Gavrilov -- 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] minimization and simulation problems
Quoting pol...@fh.huji.ac.il:
Dear gromacs users,
my box dimensions are 368A and when I run the simulation with
nsteps=1 it works fine. The mdp files used for minimization and
post-em simulation are attached.
Thanks again for your help.
Regina
Quoting chris.ne...@utoronto.ca:
What are your initial box dimensions prior to em? Also, please copy
and paste your .mdp options. Also, what happens when you run the
same post-em simulation with nsteps=1 ?
-- original message --
Dear all,
I'm trying to run simulation of 30 proteins in water using the Martini
force field. I used water.gro file in order to solvate the proteins.
For minimization I used the em.mdp file published at Martini site
(http://md.chem.rug.nl/cgmartini/index.php/home). When I set the emtol
parameter to 10 the system can't converge. So I used emtol 100 and
then the system converged. I use it as an input for the simulation.
The file can't be attached as it is too big nut I can send it if needed.
However, the sumulation crushes when I'm trying to run MD using md.mdp
also from the Martini site. I'm getting the following warnings and
errors:
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the
x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[0]={ nan, nan, nan}
Box[1]={ nan, nan, nan}
Box[2]={ nan, nan, nan}
Can not fix pbc.
---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
---
It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 0 out of 8
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0[cli_0]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
---
Program mdrun_mpi, VERSION 4.0.3
Source code file: nsgrid.c, line: 348
Fatal error:
Number of grid cells is zero. Probably the system and box collapsed.
---
Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 1 out of 8
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3[cli_3]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5[cli_5]:
aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5
gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4[cli_4]:
aborting job:
application called
[gmx-users] minimization and simulation problems
Can you please redo the md part with gen_vel=yes and see if that makes
any difference?
Generally, you need to narrow down the problem for us. Does it crash in
serial as well as parallel? How many steps does it go before the crash?
what happens to the system volume as a function of time for the duration
of the simulation prior to the crash.
Chris.
Quoting politr at fh.huji.ac.il
http://lists.gromacs.org/mailman/listinfo/gmx-users:
Dear gromacs users,
/ my box dimensions are 368A and when I run the simulation with
// nsteps=1 it works fine. The mdp files used for minimization and
// post-em simulation are attached.
/Thanks again for your help.
Regina
/
//
// Quotingchris.neale at utoronto.ca
http://lists.gromacs.org/mailman/listinfo/gmx-users:
//
// What are your initial box dimensions prior to em? Also, please copy
// and paste your .mdp options. Also, what happens when you run the
// same post-em simulation with nsteps=1 ?
//
// -- original message --
//
//
// Dear all,
// I'm trying to run simulation of 30 proteins in water using the Martini
// force field. I used water.gro file in order to solvate the proteins.
// For minimization I used the em.mdp file published at Martini site
// (http://md.chem.rug.nl/cgmartini/index.php/home). When I set the emtol
// parameter to 10 the system can't converge. So I used emtol 100 and
// then the system converged. I use it as an input for the simulation.
// The file can't be attached as it is too big nut I can send it if needed.
// However, the sumulation crushes when I'm trying to run MD using md.mdp
// also from the Martini site. I'm getting the following warnings and
// errors:
// Warning: Only triclinic boxes with the first vector parallel to the
// x-axis and the second vector in the xy-plane are supported.
// Box (3x3):
// Box[0]={ nan, nan, nan}
// Box[1]={ nan, nan, nan}
// Box[2]={ nan, nan, nan}
// Can not fix pbc.
// Warning: Only triclinic boxes with the first vector parallel to the
// x-axis and the second vector in the xy-plane are supported.
// Box (3x3):
// Box[0]={ nan, nan, nan}
// Box[1]={ nan, nan, nan}
// Box[2]={ nan, nan, nan}
// Can not fix pbc.
// Warning: Only triclinic boxes with the first vector parallel to the
// x-axis and the second vector in the xy-plane are supported.
// Box (3x3):
// Box[0]={ nan, nan, nan}
// Box[1]={ nan, nan, nan}
// Box[2]={ nan, nan, nan}
// Can not fix pbc.
// Warning: Only triclinic boxes with the first vector parallel to the
// x-axis and the second vector in the xy-plane are supported.
// Box (3x3):
// Box[0]={ nan, nan, nan}
// Box[1]={ nan, nan, nan}
// Box[2]={ nan, nan, nan}
// Can not fix pbc.
// Warning: Only triclinic boxes with the first vector parallel to the
// x-axis and the second vector in the xy-plane are supported.
// Box (3x3):
// Box[0]={ nan, nan, nan}
// Box[1]={ nan, nan, nan}
// Box[2]={ nan, nan, nan}
// Can not fix pbc.
// Warning: Only triclinic boxes with the first vector parallel to the
// x-axis and the second vector in the xy-plane are supported.
// Box (3x3):
// Box[0]={ nan, nan, nan}
// Box[1]={ nan, nan, nan}
// Box[2]={ nan, nan, nan}
// Can not fix pbc.
//
// ---
// Program mdrun_mpi, VERSION 4.0.3
// Source code file: nsgrid.c, line: 348
//
// Fatal error:
// Number of grid cells is zero. Probably the system and box collapsed.
//
// ---
//
// It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
//
// Error on node 0, will try to stop all the nodes
// Halting parallel program mdrun_mpi on CPU 0 out of 8
//
// gcq#166: It Wouldn't Hurt to Wipe Once In a While (Beavis and Butthead)
//
// application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0[cli_0]:
// aborting job:
// application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
//
// ---
// Program mdrun_mpi, VERSION 4.0.3
// Source code file: nsgrid.c, line: 348
//
// Fatal error:
// Number of grid cells is zero.
Re: [gmx-users] FEP and loss of performance
Luca Bellucci wrote: Dear Chris and Justin Thank you for your precious suggestions This is a test that i perform in a single machine with 8 cores and gromacs 4.5.4. I am trying to enhance the sampling of a protein using the decoupling scheme of the free energy module of gromacs. However when i decouple only the protein, the protein collapsed. Because i simulated in NVT i thought that this was an effect of the solvent. I was trying to decouple also the solvent to understand the system behavior. Rather than suspect that the solvent is the problem, it's more likely that decoupling an entire protein simply isn't stable. I have never tried anything that enormous, but the volume change in the system could be unstable, along with any number of factors, depending on how you approach it. If you're looking for better sampling, REMD is a much more robust approach than trying to manipulate the interactions of huge parts of your system using the free energy code. -Justin I expected a loss of performance, but not so drastic. Luca Load balancing problems I can understand, but why would it take longer in absolute time? I would have thought that some nodes would simple be sitting idle, but this should not cause an increase in the overall simulation time (15x at that!). There must be some extra communication? I agree with Justin that this seems like a strange thing to do, but still I think that there must be some underlying coding issue (probably one that only exists because of a reasonable assumption that nobody would annihilate the largest part of their system). Chris. Luca Bellucci wrote: / Hi Chris, // thank for the suggestions, // in the previous mail there is a mistake because // couple-moltype = SOL (for solvent) and not Protein_chaim_P. // Now the problem of the load balance seems reasonable, because // the water box is large ~9.0 nm. / Now your outcome makes a lot more sense. You're decoupling all of the solvent? I don't see how that is going to be physically stable or terribly meaningful, but it explains your performance loss. You're annihilating a significant number of interactions (probably the vast majority of all the nonbonded interactions in the system), which I would expect would cause continuous load balancing issues. -Justin / However the problem exist and the performance loss is very high, so I have // redone calculations with this command: // // grompp -f // md.mdp -c ../Run-02/confout.gro -t ../Run-02/state.cpt -p ../topo.top -n ../index.ndx -o // md.tpr -maxwarn 1 // // mdrun -s md.tpr -o md // // this is part of the md.mdp file: // // ; Run parameters // ; define = -DPOSRES // integrator = md; // nsteps = 1000 ; // dt = 0.002 ; // [..] // free_energy= yes ; /no // init_lambda= 0.9 // delta_lambda = 0.0 // couple-moltype = SOL; solvent water // couple-lambda0 = vdw-q // couple-lambda1 = none // couple-intramol= yes // // Result for free energy calculation // Computing: Nodes Number G-CyclesSeconds % // --- // Domain decomp. 8126 22.0508.3 0.1 // DD comm. load 8 150.0090.0 0.0 // DD comm. bounds 8 120.0310.0 0.0 // Comm. coord.8 1001 17.3196.5 0.0 // Neighbor search8127 436.569 163.7 1.1 // Force 8 100134241.57612840.9 87.8 // Wait + Comm. F8 1001 19.4867.3 0.0 // PME mesh 8 1001 4190.758 1571.6 10.7 // Write traj. 8 71.827 0.7 0.0 // Update 8 1001 12.557 4.7 0.0 // Constraints 8 1001 26.496 9.9 0.1 // Comm. energies 8 1002 10.710 4.0 0.0 // Rest 8 25.142 9.4 0.1 // --- // Total 8 39004.53114627.1 100.0 // --- // --- // PME redist. X/F 8 3003 3479.771 1304.9 8.9 // PME spread/gather 8 4004 277.574 104.1 0.7 // PME 3D-FFT 8 4004 378.090 141.8 1.0 // PME solve 8 2002 55.033 20.6 0.1 // --- // Parallel run - timing based on wallclock. // // NODE (s) Real (s) (%) // Time: 1828.385 1828.385
[gmx-users] FEP and loss of performance
Dear Chris and Justin / Thank you for your precious suggestions // This is a test that i perform in a single machine with 8 cores // and gromacs 4.5.4. // // I am trying to enhance the sampling of a protein using the decoupling scheme // of the free energy module of gromacs. However when i decouple only the // protein, the protein collapsed. Because i simulated in NVT i thought that // this was an effect of the solvent. I was trying to decouple also the solvent // to understand the system behavior. // / Rather than suspect that the solvent is the problem, it's more likely that decoupling an entire protein simply isn't stable. I have never tried anything that enormous, but the volume change in the system could be unstable, along with any number of factors, depending on how you approach it. If you're looking for better sampling, REMD is a much more robust approach than trying to manipulate the interactions of huge parts of your system using the free energy code. Presumably Luca is interested in some type of hamiltonian exchange where lambda represents the interactions between the protein and the solvent? This can actually be a useful method for enhancing sampling. I think it's dangerous if we rely to heavily on try something else. I still see no methodological reason a priori why there should be any actual slowdown, so that makes me think that it's an implementation thing, and there is at least the possibility that this is something that could be fixed as an enhancement. Chris. -Justin / I expected a loss of performance, but not so drastic. // Luca // // Load balancing problems I can understand, but why would it take longer // in absolute time? I would have thought that some nodes would simple be // sitting idle, but this should not cause an increase in the overall // simulation time (15x at that!). // // There must be some extra communication? // // I agree with Justin that this seems like a strange thing to do, but // still I think that there must be some underlying coding issue (probably // one that only exists because of a reasonable assumption that nobody // would annihilate the largest part of their system). // // Chris. // // Luca Bellucci wrote: // / Hi Chris, // // thank for the suggestions, // // in the previous mail there is a mistake because // // couple-moltype = SOL (for solvent) and not Protein_chaim_P. // // Now the problem of the load balance seems reasonable, because // // the water box is large ~9.0 nm. // / // Now your outcome makes a lot more sense. You're decoupling all of the // solvent? I don't see how that is going to be physically stable or terribly / -- 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] FEP and loss of performance
Chris Neale wrote: Dear Chris and Justin / Thank you for your precious suggestions // This is a test that i perform in a single machine with 8 cores // and gromacs 4.5.4. // // I am trying to enhance the sampling of a protein using the decoupling scheme // of the free energy module of gromacs. However when i decouple only the // protein, the protein collapsed. Because i simulated in NVT i thought that // this was an effect of the solvent. I was trying to decouple also the solvent // to understand the system behavior. // / Rather than suspect that the solvent is the problem, it's more likely that decoupling an entire protein simply isn't stable. I have never tried anything that enormous, but the volume change in the system could be unstable, along with any number of factors, depending on how you approach it. If you're looking for better sampling, REMD is a much more robust approach than trying to manipulate the interactions of huge parts of your system using the free energy code. Presumably Luca is interested in some type of hamiltonian exchange where lambda represents the interactions between the protein and the solvent? This can actually be a useful method for enhancing sampling. I think it's dangerous if we rely to heavily on try something else. I still see no methodological reason a priori why there should be any actual slowdown, so that makes me think that it's an implementation thing, and there is at least the possibility that this is something that could be fixed as an enhancement. Then perhaps we can get some clarification. Based on the earlier .mdp snippet: free_energy= yes init_lambda= 0.9 delta_lambda = 0.0 couple-moltype = Protein_Chain_P couple-lambda0 = vdw-q couple-lambda0 = none couple-intramol= yes It looked to me as if the intent was to decouple some protein complex from the system by simultaneously annihilating all solute-solvent and solute-solute nonbonded interactions (which comes with its own set of methodological issues - stability, convergence, etc). -Justin Chris. -Justin / I expected a loss of performance, but not so drastic. // Luca // // Load balancing problems I can understand, but why would it take longer // in absolute time? I would have thought that some nodes would simple be // sitting idle, but this should not cause an increase in the overall // simulation time (15x at that!). // // There must be some extra communication? // // I agree with Justin that this seems like a strange thing to do, but // still I think that there must be some underlying coding issue (probably // one that only exists because of a reasonable assumption that nobody // would annihilate the largest part of their system). // // Chris. // // Luca Bellucci wrote: // / Hi Chris, // // thank for the suggestions, // // in the previous mail there is a mistake because // // couple-moltype = SOL (for solvent) and not Protein_chaim_P. // // Now the problem of the load balance seems reasonable, because // // the water box is large ~9.0 nm. // / // Now your outcome makes a lot more sense. You're decoupling all of the // solvent? I don't see how that is going to be physically stable or terribly / -- 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/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] autocorrelation functions
Hello all, I need to calculate the end-to-end vector autocorrelation function of my polymer chains. I could get the velocity autocorrelation function using g_velacc tool. Is there a tool available for calculating end-to-end vector autocorrelation function? If not, then is there an easy way to modify/morph the g_velacc.c program to do other autocorrelation function calculations? Thanks, SN -- 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] how to Installing GROMACS in rocks cluster
Dear Colleagues. I have been searching information about HOW TO INSTALL GROMACS in rocks cluster?. Unfortunately, the information that I found is not clear. Someone can help me with this question. Maybe there are basic but important steps that I have to keep in mind. Could you please share yours experiences? Thank you in advance. Miguel Quiliano. P.D I have installed rocks cluster 5.4 -- 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] autocorrelation functions
Hello all, I need to calculate the end-to-end vector autocorrelation function of my polymer chains. I could get the velocity autocorrelation function using g_velacc tool. Is there a tool available for calculating end-to-end vector autocorrelation function? If not, then is there an easy way to modify/morph the g_velacc.c program to do other autocorrelation function calculations? Thanks, Shivangi -- 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] FEP and loss of performance
Yes i am testing the possibility to perform an Hamiltonian-REMD Energy barriers can be overcome increasing the temperature system or scaling potential energy with a lambda value, these methods are equivalent. Both have advantages and disavantages, at this stage it is not the right place to debate on it. The main problem seems to be how to overcome to the the loss of gromacs performance in such calculation. At this moment it seems an intrinsic code problem. Is it possible? Dear Chris and Justin / Thank you for your precious suggestions // This is a test that i perform in a single machine with 8 cores // and gromacs 4.5.4. // // I am trying to enhance the sampling of a protein using the decoupling scheme // of the free energy module of gromacs. However when i decouple only the // protein, the protein collapsed. Because i simulated in NVT i thought that // this was an effect of the solvent. I was trying to decouple also the solvent // to understand the system behavior. // / Rather than suspect that the solvent is the problem, it's more likely that decoupling an entire protein simply isn't stable. I have never tried anything that enormous, but the volume change in the system could be unstable, along with any number of factors, depending on how you approach it. If you're looking for better sampling, REMD is a much more robust approach than trying to manipulate the interactions of huge parts of your system using the free energy code. Presumably Luca is interested in some type of hamiltonian exchange where lambda represents the interactions between the protein and the solvent? This can actually be a useful method for enhancing sampling. I think it's dangerous if we rely to heavily on try something else. I still see no methodological reason a priori why there should be any actual slowdown, so that makes me think that it's an implementation thing, and there is at least the possibility that this is something that could be fixed as an enhancement. Chris. -Justin / I expected a loss of performance, but not so drastic. // Luca // // Load balancing problems I can understand, but why would it take longer // in absolute time? I would have thought that some nodes would simple be // sitting idle, but this should not cause an increase in the overall // simulation time (15x at that!). // // There must be some extra communication? // // I agree with Justin that this seems like a strange thing to do, but // still I think that there must be some underlying coding issue (probably // one that only exists because of a reasonable assumption that nobody // would annihilate the largest part of their system). // // Chris. // // Luca Bellucci wrote: // / Hi Chris, // // thank for the suggestions, // // in the previous mail there is a mistake because // // couple-moltype = SOL (for solvent) and not Protein_chaim_P. // // Now the problem of the load balance seems reasonable, because // // the water box is large ~9.0 nm. // / // Now your outcome makes a lot more sense. You're decoupling all of the // solvent? I don't see how that is going to be physically stable or terribly / -- 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] g_chi
Hi, I have 2 questions on using g_chi to calculate only one omega angle for X-Pro. 1. I used the following command: g_chi -s md.gro/tpr -f md.xtc -omega -o test.xvg and got the following message: Fatal error: Library file in current dir nor not found aminoacids.datin default directories. (You can set the directories to search with the GMXLIB path variable) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors; 2. The command does not allow using index file. How can I calculate just one dihedral angle? Thanks for your help in advance. Simon Sham -- 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] g_chi
Hi Simon, Regarding the first question you should set GMXLIB as $GMXDATA/gromacs/top. I don't know how to solve the second problem bacause I never used g_chi Il 04/04/2011 22:19, simon sham ha scritto: Hi, I have 2 questions on using g_chi to calculate only one omega angle for X-Pro. 1. I used the following command: g_chi -s md.gro/tpr -f md.xtc -omega -o test.xvg and got the following message: Fatal error: Library file in current dir nor not found aminoacids.datin default directories. (You can set the directories to search with the GMXLIB path variable) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors; 2. The command does not allow using index file. How can I calculate just one dihedral angle? Thanks for your help in advance. Simon Sham -- 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] g_chi
simon sham wrote: Hi, I have 2 questions on using g_chi to calculate only one omega angle for X-Pro. 1. I used the following command: g_chi -s md.gro/tpr -f md.xtc -omega -o test.xvg and got the following message: Fatal error: Library file in current dir nor not found aminoacids.datin default directories. (You can set the directories to search with the GMXLIB path variable) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors; Upgrade to a newer version of Gromacs. This bug has been fixed. 2. The command does not allow using index file. How can I calculate just one dihedral angle? Not sure on this one, but once you have a properly-functioning executable, you should be able to tell from the output files (of which there is a .log file that should contain everything). -Justin Thanks for your help in advance. Simon Sham -- 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/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] Postdoc position available
Hi all, A post-doctoral research position is available at Northwestern University at Evanston, IL. The position is in the field of computational physical chemistry, with a focus on molecular dynamics simulation and force field development. The systems to be studied include water/air, water/ice and ice/air interfaces, and the chemical processes occurring at these interfaces. The candidate must have a Ph.D. in chemistry or physics, excellent practical and theoretical understanding of atomistic simulation methods, programming experience and working experience in a Linux environment. The candidate must also be able to prepare manuscripts and present ongoing research. For further information please contact: Marcelo Carignano c...@northwestern.edu -- 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] coordination number and g_analysis
Hello, I want to calculat the coordination number of solute in first solvation shell. integration of (4*pi*r^2*g(r)) from 0 to 2.6 A(first solvation shell) If I calcualte the g_rdf for first solvation shell (till 2.6 A) and then I integrate this using g_analysis. Can I go this way. Nilesh -- 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: gmx-users Digest, Vol 84, Issue 28
Dear colleagues. I would like to share with the community this. Searching I can find this: http://software.intel.com/en-us/articles/compile-and-run-gromacs-453-in-icr/ Compile and run GROMACS 4.5.3 in the Intel(R) Cluster Ready Reference Recipe S5520UR-ICR1.1-ROCKS5.3-CENTOS5.4-C2 v1.0I think is very useful for People who have the same objective. However, in one section the tutorial refers that the GROMACS version 4.5.3 had some bugs. I would like to install version GROMACS 4.5.4, Does somebody know if this version has the same problems? Thanks in advance. Miguel Quiliano. 2011/4/4 gmx-users-requ...@gromacs.org Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. how to Installing GROMACS in rocks cluster (Miguel Quiliano Meza) 2. autocorrelation functions (shivangi nangia) 3. Re: FEP and loss of performance (Luca Bellucci) 4. g_chi (simon sham) 5. Re: g_chi (Francesco Oteri) 6. Re: g_chi (Justin A. Lemkul) -- Message: 1 Date: Mon, 4 Apr 2011 13:58:40 -0400 From: Miguel Quiliano Meza rifaxim...@gmail.com Subject: [gmx-users] how to Installing GROMACS in rocks cluster To: gmx-users@gromacs.org Message-ID: BANLkTimh_Lx_E9B=fJ-WRypK-vh=cf2...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Dear Colleagues. I have been searching information about HOW TO INSTALL GROMACS in rocks cluster?. Unfortunately, the information that I found is not clear. Someone can help me with this question. Maybe there are basic but important steps that I have to keep in mind. Could you please share yours experiences? Thank you in advance. Miguel Quiliano. P.D I have installed rocks cluster 5.4 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110404/ef4b39fe/attachment-0001.html -- Message: 2 Date: Mon, 4 Apr 2011 14:11:48 -0400 From: shivangi nangia shivangi.nan...@gmail.com Subject: [gmx-users] autocorrelation functions To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: BANLkTi=HS9T7zpWkhEVFsYmZjrV=he1...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hello all, I need to calculate the end-to-end vector autocorrelation function of my polymer chains. I could get the velocity autocorrelation function using g_velacc tool. Is there a tool available for calculating end-to-end vector autocorrelation function? If not, then is there an easy way to modify/morph the g_velacc.c program to do other autocorrelation function calculations? Thanks, Shivangi -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110404/cb2a4e0a/attachment-0001.html -- Message: 3 Date: Mon, 4 Apr 2011 20:36:37 +0200 From: Luca Bellucci lcbl...@gmail.com Subject: Re: [gmx-users] FEP and loss of performance To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 201104042036.37450.lcbl...@gmail.com Content-Type: text/plain; charset=utf-8 Yes i am testing the possibility to perform an Hamiltonian-REMD Energy barriers can be overcome increasing the temperature system or scaling potential energy with a lambda value, these methods are equivalent. Both have advantages and disavantages, at this stage it is not the right place to debate on it. The main problem seems to be how to overcome to the the loss of gromacs performance in such calculation. At this moment it seems an intrinsic code problem. Is it possible? Dear Chris and Justin / Thank you for your precious suggestions // This is a test that i perform in a single machine with 8 cores // and gromacs 4.5.4. // // I am trying to enhance the sampling of a protein using the decoupling scheme // of the free energy module of gromacs. However when i decouple only the // protein, the protein collapsed. Because i simulated in NVT i thought that // this was an effect of the solvent. I was trying to decouple also the solvent // to understand the system behavior. // / Rather than suspect that the solvent is the problem, it's more likely that decoupling an entire protein simply isn't stable. I have never tried anything that enormous, but the volume change in the system could be unstable, along with any number of factors, depending on how you approach
Re: [gmx-users] Re: gmx-users Digest, Vol 84, Issue 28
Miguel Quiliano Meza wrote: Dear colleagues. I would like to share with the community this. Searching I can find this: http://software.intel.com/en-us/articles/compile-and-run-gromacs-453-in-icr/ Compile and run GROMACS 4.5.3 in the Intel(R) Cluster Ready Reference Recipe S5520UR-ICR1.1-ROCKS5.3-CENTOS5.4-C2 v1.0 I think is very useful for People who have the same objective. However, in one section the tutorial refers that the GROMACS version 4.5.3 had some bugs. I would like to install version GROMACS 4.5.4, Does somebody know if this version has the same problems? It was fixed for 4.5.4. -Justin Thanks in advance. Miguel Quiliano. 2011/4/4 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org Send gmx-users mailing list submissions to gmx-users@gromacs.org mailto:gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org mailto:gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. how to Installing GROMACS in rocks cluster (Miguel Quiliano Meza) 2. autocorrelation functions (shivangi nangia) 3. Re: FEP and loss of performance (Luca Bellucci) 4. g_chi (simon sham) 5. Re: g_chi (Francesco Oteri) 6. Re: g_chi (Justin A. Lemkul) -- Message: 1 Date: Mon, 4 Apr 2011 13:58:40 -0400 From: Miguel Quiliano Meza rifaxim...@gmail.com mailto:rifaxim...@gmail.com Subject: [gmx-users] how to Installing GROMACS in rocks cluster To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: BANLkTimh_Lx_E9B=fJ-WRypK-vh=cf2...@mail.gmail.com mailto:cf2...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Dear Colleagues. I have been searching information about HOW TO INSTALL GROMACS in rocks cluster?. Unfortunately, the information that I found is not clear. Someone can help me with this question. Maybe there are basic but important steps that I have to keep in mind. Could you please share yours experiences? Thank you in advance. Miguel Quiliano. P.D I have installed rocks cluster 5.4 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110404/ef4b39fe/attachment-0001.html -- Message: 2 Date: Mon, 4 Apr 2011 14:11:48 -0400 From: shivangi nangia shivangi.nan...@gmail.com mailto:shivangi.nan...@gmail.com Subject: [gmx-users] autocorrelation functions To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: BANLkTi=HS9T7zpWkhEVFsYmZjrV=he1...@mail.gmail.com mailto:he1...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hello all, I need to calculate the end-to-end vector autocorrelation function of my polymer chains. I could get the velocity autocorrelation function using g_velacc tool. Is there a tool available for calculating end-to-end vector autocorrelation function? If not, then is there an easy way to modify/morph the g_velacc.c program to do other autocorrelation function calculations? Thanks, Shivangi -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110404/cb2a4e0a/attachment-0001.html -- Message: 3 Date: Mon, 4 Apr 2011 20:36:37 +0200 From: Luca Bellucci lcbl...@gmail.com mailto:lcbl...@gmail.com Subject: Re: [gmx-users] FEP and loss of performance To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 201104042036.37450.lcbl...@gmail.com mailto:201104042036.37450.lcbl...@gmail.com Content-Type: text/plain; charset=utf-8 Yes i am testing the possibility to perform an Hamiltonian-REMD Energy barriers can be overcome increasing the temperature system or scaling potential energy with a lambda value, these methods are equivalent. Both have advantages and disavantages, at this stage it is not the right place to debate on it. The main problem seems to be how to overcome to the the loss of gromacs performance in such calculation. At this moment it seems an intrinsic code problem. Is it possible? Dear Chris and Justin / Thank you for your precious suggestions
Re: [gmx-users] coordination number and g_analysis
I'll rather use: g_rdf -cn Marcelo. On Apr 4, 2011, at 4:17 PM, Nilesh Dhumal wrote: Hello, I want to calculat the coordination number of solute in first solvation shell. integration of (4*pi*r^2*g(r)) from 0 to 2.6 A(first solvation shell) If I calcualte the g_rdf for first solvation shell (till 2.6 A) and then I integrate this using g_analysis. Can I go this way. Nilesh -- 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] Splitted DMPC bilayer
Justin, Thank you for your comments after finishing the MD production run for up to 20 ns... Since this step was over very quickly, now I have a simple question ¿How long, in human time, should a production run last? The production run was carried out in six processors Intel Xeon (R) E5405 2.00 GHz. The last few lines of the md_0_1.log are: - Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 180685.417 180685.417100.0 2d02h11:25 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:232.900 12.351 9.564 2.510 - Is this correct? In my opinion it should lasted much more longer... Before reaching this point, this is an update of what we did... First we eliminated the SOL_SOL group and the only special index group was Protein_DMPC. Since the NVT equilibration failed, we took option # 2 of the Advanced Troubleshooting, for the 1st phase of Equilibration. After this step we proceeded with the equilibration phase 2 with a 1-ns NPT equilibration which ended fine. Next, we proceeded with a 20 ns production run. Thus, the modified lines of the .mpd file found in the tutorial page were: nsteps = 1000 ; 2 * 1000 = 2000 ps (20 ns) tc-grps = Protein DMPC SOL comm-grps = Protein_DMPC SOL With this instructions the 20 ns simulation took 2d02h11:25 I believe the error comes from the line constrains = all-bonds which surely must be changed to constrains = none or hbonds Looking forward to your comments... Much obliged, Ramon El 30/03/2011 12:25 p.m., Justin A. Lemkul escribió: Dr. Ramón Garduño-Juárez wrote: Dear all, Dear Justin, This time I want to ask the gurus about this problem I encountered in the Equilibration step of my system made of 3 individual (small) protein chains in a solvated DMPC bilayer, no ions present since the protein system is neutral... Following the tutorial I started with make_ndx_d -f em_after_solv.gro -o index_after_solv.ndx for which I got the following list: - Reading structure file Going to read 0 old index file(s) Analysing residue names: There are: 129Protein residues There are: 123 Other residues There are: 3215 Water residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 0 System : 16649 atoms 1 Protein : 1346 atoms 2 Protein-H : 1025 atoms 3 C-alpha : 129 atoms 4 Backbone: 387 atoms 5 MainChain : 519 atoms 6 MainChain+Cb: 636 atoms 7 MainChain+H : 649 atoms 8 SideChain : 697 atoms 9 SideChain-H : 506 atoms 10 Prot-Masses : 1346 atoms 11 non-Protein : 15303 atoms 12 Other : 5658 atoms 13 DMPC: 5658 atoms 14 Water : 9645 atoms 15 SOL : 9645 atoms 16 non-Water : 7004 atoms - Since I did not add ions I have formed a (merged) group named SOL_SOL Why would you merge solvent with itself? after chosing 15 | 15 , and another merged group named Protein_DMPC by choosing 1 | 13... Next, I started the NVT equilibration with: grompp_d -f nvt.mdp -c em_after_solv.gro -p topol_mod_lip_solv.top -n index_after_solv.ndx -o nvt.tpr The nvt.mpd file is the same as the one given in the tutorial, the only changes I made were: tc-grps= Protein DMPC SOL_SOL and comm-grps= Protein_DMPC SOL_SOL I would think that using this weird SOL_SOL group would create problems related to degrees of freedom, etc. If you have no ions, there is no need to merge any sort of solvent-related groups. After this I ran mdrun_mpi_d -v -deffnm nvt When this process is finished I looked at the resulting nvt.gro file and found the following: 1) The 3 protein chains complex is fine, at the center of the box as it should be, but 2) The 2 DMPC layer are separated (splitted) leaving a large gap between them forming a )( shape where the top and bottom of this figure contain one layer of DMPC plus water molecules, while in the narrow section the protein complex is found... In the void between the two DMPC layers no water molecules are present... Very odd!... Please advice... This is covered in the Advanced Troubleshooting section of my tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/advanced_troubleshooting.html -Justin Cheers, Ramon Garduno attachment: ramon.vcf-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the
Re: [gmx-users] Splitted DMPC bilayer
Dr. Ramón Garduño-Juárez wrote: Justin, Thank you for your comments after finishing the MD production run for up to 20 ns... Since this step was over very quickly, now I have a simple question ¿How long, in human time, should a production run last? There is no way to answer that. It depends on the hardware, number of atoms, system load, application of any number of the Gromacs algorithms, .mdp settings... The production run was carried out in six processors Intel Xeon (R) E5405 2.00 GHz. The last few lines of the md_0_1.log are: - Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 180685.417 180685.417100.0 2d02h11:25 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:232.900 12.351 9.564 2.510 - Is this correct? In my opinion it should lasted much more longer... Nope, Gromacs is just fast :) Before reaching this point, this is an update of what we did... First we eliminated the SOL_SOL group and the only special index group was Protein_DMPC. Since the NVT equilibration failed, we took option # 2 of the Advanced Troubleshooting, for the 1st phase of Equilibration. After this step we proceeded with the equilibration phase 2 with a 1-ns NPT equilibration which ended fine. Next, we proceeded with a 20 ns production run. Thus, the modified lines of the .mpd file found in the tutorial page were: nsteps = 1000 ; 2 * 1000 = 2000 ps (20 ns) tc-grps = Protein DMPC SOL comm-grps = Protein_DMPC SOL With this instructions the 20 ns simulation took 2d02h11:25 I believe the error comes from the line constrains = all-bonds which surely must be changed to constrains = none or hbonds Why do you say that? What error is occurring? You said your simulations were running fine. You most certainly should not remove constraints if you're sticking with a 2-fs timestep. The system will be unstable without constraints. You might be able to get away with hbonds, but certainly not none. -Justin Looking forward to your comments... Much obliged, Ramon El 30/03/2011 12:25 p.m., Justin A. Lemkul escribió: Dr. Ramón Garduño-Juárez wrote: Dear all, Dear Justin, This time I want to ask the gurus about this problem I encountered in the Equilibration step of my system made of 3 individual (small) protein chains in a solvated DMPC bilayer, no ions present since the protein system is neutral... Following the tutorial I started with make_ndx_d -f em_after_solv.gro -o index_after_solv.ndx for which I got the following list: - Reading structure file Going to read 0 old index file(s) Analysing residue names: There are: 129Protein residues There are: 123 Other residues There are: 3215 Water residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 0 System : 16649 atoms 1 Protein : 1346 atoms 2 Protein-H : 1025 atoms 3 C-alpha : 129 atoms 4 Backbone: 387 atoms 5 MainChain : 519 atoms 6 MainChain+Cb: 636 atoms 7 MainChain+H : 649 atoms 8 SideChain : 697 atoms 9 SideChain-H : 506 atoms 10 Prot-Masses : 1346 atoms 11 non-Protein : 15303 atoms 12 Other : 5658 atoms 13 DMPC: 5658 atoms 14 Water : 9645 atoms 15 SOL : 9645 atoms 16 non-Water : 7004 atoms - Since I did not add ions I have formed a (merged) group named SOL_SOL Why would you merge solvent with itself? after chosing 15 | 15 , and another merged group named Protein_DMPC by choosing 1 | 13... Next, I started the NVT equilibration with: grompp_d -f nvt.mdp -c em_after_solv.gro -p topol_mod_lip_solv.top -n index_after_solv.ndx -o nvt.tpr The nvt.mpd file is the same as the one given in the tutorial, the only changes I made were: tc-grps= Protein DMPC SOL_SOL and comm-grps= Protein_DMPC SOL_SOL I would think that using this weird SOL_SOL group would create problems related to degrees of freedom, etc. If you have no ions, there is no need to merge any sort of solvent-related groups. After this I ran mdrun_mpi_d -v -deffnm nvt When this process is finished I looked at the resulting nvt.gro file and found the following: 1) The 3 protein chains complex is fine, at the center of the box as it should be, but 2) The 2 DMPC layer are separated (splitted) leaving a large gap between them forming a )( shape where the top and bottom of this figure contain one layer of DMPC plus water
[gmx-users] g_chi
Hi, Thanks for those who replied my previous questions on g_chi. I just installed the latest version of gromacs 4.5.4 and could run the command. I still have a question about the command: Again, I used the following command: g_chi -s md.tpr -f md.xtc -omega It generated a series of xmgrace files for each residue, but it does not give a residue #. In the chi.log file, it only listed the four omega atom numbers for each residue...that's it. Again thanks for your help in advance. Simon Sham -- 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] Splitted DMPC bilayer
Justin, Again much obliged for your comments. They are most illustrative... I would like to make a final note on the issue of these many e-mails... I am sure that GROMACS is fast, but that fast?... For the sake of knowing that we are doing the right things, this is our topol.top file in which we eliminated all POSRES for the Protein and DMPC, not so for the WATER... - ; Include forcefield parameters #include ./gromos53a6_lipid.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp #include topol_Protein_chain_C.itp ; Include water topology #include ./gromos53a6_lipid.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include ./gromos53a6_lipid.ff/ions.itp [ system ] ; Name mod.pdb [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 Protein_chain_C 1 -- On Protein_chain_A there are 342 atoms On Protein_chain_B there are 289 atoms On Protein_chain_C there are 715 atoms On DMPC there are 123 molecules of 46 atoms each On SOL there are 3205 molecules of 3 atoms each For a total of 16619 atoms I know that this is a medium size system for which I was expecting longer CPU time for a 20 ns MD run. I know that there was no error, which I meant is that I was surprised by the outcome... May be GROMACS is as fast as it is claimed... Cheers, Ramon El 04/04/2011 05:27 p.m., Justin A. Lemkul escribió: Dr. Ramón Garduño-Juárez wrote: Justin, Thank you for your comments after finishing the MD production run for up to 20 ns... Since this step was over very quickly, now I have a simple question ¿How long, in human time, should a production run last? There is no way to answer that. It depends on the hardware, number of atoms, system load, application of any number of the Gromacs algorithms, .mdp settings... The production run was carried out in six processors Intel Xeon (R) E5405 2.00 GHz. The last few lines of the md_0_1.log are: - Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 180685.417 180685.417100.0 2d02h11:25 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:232.900 12.351 9.564 2.510 - Is this correct? In my opinion it should lasted much more longer... Nope, Gromacs is just fast :) Before reaching this point, this is an update of what we did... First we eliminated the SOL_SOL group and the only special index group was Protein_DMPC. Since the NVT equilibration failed, we took option # 2 of the Advanced Troubleshooting, for the 1st phase of Equilibration. After this step we proceeded with the equilibration phase 2 with a 1-ns NPT equilibration which ended fine. Next, we proceeded with a 20 ns production run. Thus, the modified lines of the .mpd file found in the tutorial page were: nsteps = 1000 ; 2 * 1000 = 2000 ps (20 ns) tc-grps = Protein DMPC SOL comm-grps = Protein_DMPC SOL With this instructions the 20 ns simulation took 2d02h11:25 I believe the error comes from the line constrains = all-bonds which surely must be changed to constrains = none or hbonds Why do you say that? What error is occurring? You said your simulations were running fine. You most certainly should not remove constraints if you're sticking with a 2-fs timestep. The system will be unstable without constraints. You might be able to get away with hbonds, but certainly not none. -Justin Looking forward to your comments... Much obliged, Ramon attachment: ramon.vcf-- 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] Splitted DMPC bilayer
Dr. Ramón Garduño-Juárez wrote: Justin, Again much obliged for your comments. They are most illustrative... I would like to make a final note on the issue of these many e-mails... I am sure that GROMACS is fast, but that fast?... Yes. Your results prove it. With quality hardware, you get great performance. For the sake of knowing that we are doing the right things, this is our topol.top file in which we eliminated all POSRES for the Protein and DMPC, not so for the WATER... To what end, I do not know. One generally does not find much use in restraining water while everything else moves, but syntactically, it is correct. - ; Include forcefield parameters #include ./gromos53a6_lipid.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp #include topol_Protein_chain_C.itp ; Include water topology #include ./gromos53a6_lipid.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include ./gromos53a6_lipid.ff/ions.itp [ system ] ; Name mod.pdb [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 Protein_chain_C 1 -- On Protein_chain_A there are 342 atoms On Protein_chain_B there are 289 atoms On Protein_chain_C there are 715 atoms On DMPC there are 123 molecules of 46 atoms each On SOL there are 3205 molecules of 3 atoms each For a total of 16619 atoms I know that this is a medium size system for which I was expecting longer CPU time for a 20 ns MD run. I know that there was no error, which I meant is that I was surprised by the outcome... May be GROMACS is as fast as it is claimed... Indeed. -Justin Cheers, Ramon El 04/04/2011 05:27 p.m., Justin A. Lemkul escribió: Dr. Ramón Garduño-Juárez wrote: Justin, Thank you for your comments after finishing the MD production run for up to 20 ns... Since this step was over very quickly, now I have a simple question ¿How long, in human time, should a production run last? There is no way to answer that. It depends on the hardware, number of atoms, system load, application of any number of the Gromacs algorithms, .mdp settings... The production run was carried out in six processors Intel Xeon (R) E5405 2.00 GHz. The last few lines of the md_0_1.log are: - Parallel run - timing based on wallclock. NODE (s) Real (s) (%) Time: 180685.417 180685.417100.0 2d02h11:25 (Mnbf/s) (GFlops) (ns/day) (hour/ns) Performance:232.900 12.351 9.564 2.510 - Is this correct? In my opinion it should lasted much more longer... Nope, Gromacs is just fast :) Before reaching this point, this is an update of what we did... First we eliminated the SOL_SOL group and the only special index group was Protein_DMPC. Since the NVT equilibration failed, we took option # 2 of the Advanced Troubleshooting, for the 1st phase of Equilibration. After this step we proceeded with the equilibration phase 2 with a 1-ns NPT equilibration which ended fine. Next, we proceeded with a 20 ns production run. Thus, the modified lines of the .mpd file found in the tutorial page were: nsteps = 1000 ; 2 * 1000 = 2000 ps (20 ns) tc-grps = Protein DMPC SOL comm-grps = Protein_DMPC SOL With this instructions the 20 ns simulation took 2d02h11:25 I believe the error comes from the line constrains = all-bonds which surely must be changed to constrains = none or hbonds Why do you say that? What error is occurring? You said your simulations were running fine. You most certainly should not remove constraints if you're sticking with a 2-fs timestep. The system will be unstable without constraints. You might be able to get away with hbonds, but certainly not none. -Justin Looking forward to your comments... Much obliged, Ramon -- 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/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] g_chi
simon sham wrote: Hi, Thanks for those who replied my previous questions on g_chi. I just installed the latest version of gromacs 4.5.4 and could run the command. I still have a question about the command: Again, I used the following command: g_chi -s md.tpr -f md.xtc -omega It generated a series of xmgrace files for each residue, but it does not give a residue #. In the chi.log file, it only listed the four omega atom numbers for each residue...that's it. g_chi is intended for dihedral transitions and order parameters. If you just want an actual dihedral angle measurement, use g_angle. -Justin Again thanks for your help in advance. Simon Sham -- 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/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] autocorrelation functions
On 5/04/2011 2:55 AM, shivangi nangia wrote: Hello all, I need to calculate the end-to-end vector autocorrelation function of my polymer chains. I could get the velocity autocorrelation function using g_velacc tool. Is there a tool available for calculating end-to-end vector autocorrelation function? If not, then is there an easy way to modify/morph the g_velacc.c program to do other autocorrelation function calculations? Use g_dist to get the distances and then g_analyze to find the autocorrelation. 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
[gmx-users] Protein_thermal_Unfolding
Dear users, I am new to Gromacs. I am trying to study thermal unfolding of a protein having intra molecular disulfide bonds. As during simulations these bonds will not break, will I be able to study the unfolding pathway. Are there other ways to study such type of systems. S Satya Gulbraga 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/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] the total charge of system is not an integer
Dear Tsjerk, Hi Ahmet, As suggested, it's better to break up your molecule into smaller charge groups. Note that charge groups don't need to have zero charge, nor integer charge. In your case, I'd suggest two COH groups for EDO, which will have zero net charge each, and for TRS I'd take the COH groups as separate charge groups. I also note that the COH groups, although chemically identical - H3NC(COH)3, right?-, have different charges. That doesn't seem proper. Hope it helps, Tsjerk nonrevised .itp file: EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 10.080 14.0270 4 CH2 1 EDO CAC 10.080 14.0270 5OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 10.031 1.0080 nonrevised .itp file: EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0.111 15.9994 2 H 1 EDO HAE 10.031 1.0080 3 CH2 1 EDO CAA 1*0.000* 14.0270 4 CH2 1 EDO CAC 1*0.000* 14.0270 5OA 1 EDO OAD 1 -0.111 15.9994 6 H 1 EDO HAF 10.031 1.0080 can you show me on the itp file? how do I seperate two COH groups? Please help me 31 Mart 2011 12:10 tarihinde Tsjerk Wassenaar tsje...@gmail.com yazdı: Hi Ahmet, Why would I get angry? :) Sending a reply to the list will not usually be taken as asking for private tutoring... As Mark pointed out, you need to get familiar with the format of the files. That's the first thing you should do if you get to the point of needing to use non standard topologies. Read the manual, look at existing files. As for the immediate question, under the [ atoms ] section is a line indicating which column denotes what. You'd need to modify the columns 'cgnr' (charge group number) and probably 'charge'. For finding proper charge groups, in general you best draw your molecule, with the charges added, and then see which atoms would almost naturally group together. TRS.itp: .. [ moleculetype ] ; Name nrexcl TRS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 10.032 1.0080 3 CH2 1 TRS C1 10.087 14.0270 4 CCl4 1 TRS C 20.055 12.0110 5 CH2 1 TRS C3 20.049 14.0270 6OA 1 TRS O3 2 -0.205 15.9994 Hope it helps, Tsjerk 2011/3/31 ahmet yıldırım ahmedo...@gmail.com: Dear Tsjerk, I will ask you one thing but please do not get angry (I know you are not a private tutor but I need your helps). How do I apply on the files (EDO.itp and TRS.itp) that you said? (or can you suggest a tutorial?) Thanks 2011/3/31 Mark Abraham mark.abra...@anu.edu.au On 31/03/2011 5:18 PM, ahmet yıldırım wrote: Dear users, Before energy minimization step , I performed the preprosessing step using grompp . However, there are two note that : NOTE 1 [file topol.top, line 52]: System has non-zero total charge: -1.50e+01 This is an integer. See http://en.wikipedia.org/wiki/Scientific_notation#E_notation and http://www.gromacs.org/Documentation/Floating_Point_Arithmetic NOTE 2 [file topol.top]: The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. See Tsjerk's email. Mark PS: TRS and EDO are not aminoacid TRS.itp: .. [ moleculetype ] ; Name nrexcl TRS 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 TRS O1 1 -0.119 15.9994 2 H 1 TRS H13 10.032 1.0080 3 CH2 1 TRS C1 10.087 14.0270 4 CCl4 1 TRS C 20.055 12.0110 5 CH2 1 TRS C3 20.049 14.0270 6OA 1 TRS O3 2 -0.205 15.9994 7 H 1 TRS H33 20.019 1.0080 8NL 1 TRS N 20.206 14.0067 9 H 1 TRS H2 20.004 1.0080 10 H 1 TRS H3 20.004 1.0080 11 H 1 TRS H1 20.004 1.0080 12 CH2 1 TRS C2 2
