[gmx-users] Regarding multiple ligands' topology
Dear GMX users, I would like to use multiple small molecules in the simulation system. The topology files of the ligands were generated by swissparam. However, grompp could not recognize the second ligand topology during the preparation of system and gives following message: '[ atomtypes ]' Invalid order for directive atomtypes How can overcome this problem? Best regards, Mijiddorj -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] polymer & peptide interaction pbc, visualization problem
I've run protein adsorptions on PE, PEO, nylon and the like. The way I approach such models is to first model the surface. Depending on if you want an "extruded" polymer or a cast surface will define how you restrain it. For most of my models - polymer strands of about 1000 atoms, and using about 100 strands in three layers, I restrain only the ends and only in the x direction to simulate an extrusion of a much larger molecule which is normally under stress. This lets the polymer blend in the z and y direction ( x-y surface plane ). Then proceed normally through NVT, NPT to a surface that looks and reacts as normal as an MM can do e.g. do H-bonds form in Nylon, ask if water beads on PE etc. When you feel that it is representative of the surface - add it to a library of surfaces. Then add the protein. Try to replicate https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548063/ it will get you a long way toward your goal. You can add the protein much the same way the Kalp models are shown in the tutorials. Hope this helps Paul UMN , BICB On Nov 7 2019, at 9:37 am, Sezai-Raif Baydan wrote: > Hello! > > > > I am trying to simulate the adsorption of a certain peptide on a certain > polymer surface. For that, I did position restrain of polymer heavy atom and > position restrain of protein heavy atoms during the NVT and NPT equilibration > and also during energy minimization (EM). > > > The first lines of my minim.mdp file looks like this: > > > ; minim.mdp - used as input into grompp to generate em.tpr > define = -DPOSRES -DPP_POSRES > integrator = steep ; Algorithm (steep = steepest descent minimization) > constraints = none > > > > The first lines of nvt.mdp and npt.mdp looks like this: > > > define = -DPOSRES -DPP_POSRES ; position restrain the protein and polymer > ; Run parameters > integrator = md ; leap-frog integrator > nsteps = 10 ; 2 * 5 = 200 ps > dt = 0.002 ; 1 fs > > > > After the equilibration steps, I run my sytem for 100 ns. In my md.mdp file I > just include the position restrain of polymer heavy atoms. > I also include the position restrain files (posre.itp and posre_polym.itp) in > my topology file: > > ; Include polymer topology > #include "amber99sb-ildn.ff/polymer_GMX.itp" > > ; Include Position restraint file for polymer > #ifdef PP_POSRES > #include "posre_polym.itp" > #endif > > ; Include water topology > #include "./amber99sb-ildn.ff/spce.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > ; Include topology for ions > #include "./amber99sb-ildn.ff/ions.itp" > > [ system ] > ; Name > peptide and polymer in water > > [ molecules ] > ; Compound #mols > Protein_chain_A 1 > Mth 225 > SOL 8621 > CL 13 > > > > I do not get any gmx errors! I remove the pbc with: trjconv -s md_0_1.tpr -f > md_0_1.xtc -o md_0_1_noPBC.xtc -pbc -mol -center > > > When I first upload my md_0_1.gro file in VMD I can see often “artefacts”. > So, a monatomic perpendicular fraction of my layer is over my peptide. And > that means of course out of the box. But also in some .gro files, I can see a > whole monatomic layer over the peptide! Anyway they disappear once I include > my noPBC.xtc file. > > > Once I load my noPBC.xtc file, I saw that the layer is not “stable”. Because > when I act out the frames, I see that the layer is shifting over my peptide. > It is not the whole layer which is shifting and it is not all the time but in > many frames one can see these shifts. I would like to show you some > screenshots about this, but the data is too big of one screenshot. > > > I also try this invocation: trjconv -s md.tpr -f md.xtc -o md_noPBC_whole.xtc > -pbc whole -center -ur compact > trjconv -s md.tpr -f md_noPBC_whole -center -pbc mol > > > > But even then, I have the same problem as described before. > > > When I use this: trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc > -mol -ur compact > > > I do not see any shifting of my layer. But this time I cannot see any > interactions of my peptide with the layer. > > > Can somebody help me with this issue? How can I remove the pbc so I do not > have any artefacts of my layer so I can see a adsorption of my peptide? > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to
Re: [gmx-users] printing option
Thank you so much Dr. Lemkul. Hadi On Thu, Nov 7, 2019 at 2:04 PM Justin Lemkul wrote: > > > On 11/7/19 12:26 PM, Patel, Lara Anne wrote: > > Hi Hadi, > > > > > > I have only gotten prints of "stepXXX.pdb" when something is going wrong > with the simulation. That is not a printing option but rather supposed to > help you in diagnosing the problem. > > This is indeed their intended purpose. If suppressing them is really > necessary, one can do that with > > export GMX_SUPPRESS_DUMP=1 > > -Justin > > > > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Hadi > Rahmaninejad > > Sent: Thursday, November 7, 2019 10:04:58 AM > > To: gmx-us...@gromacs.org > > Subject: [gmx-users] printing option > > > > Hello gromacs users, > > > > Can any body give me a reference page in gromacs manual for printing > option > > in energy minimization? I know for nvt other steps, but in energy > > minimization it automatically prints a lot of "stepXXX.pdb" which are > > unnecessary and I want to avoid that. > > > > Thanks, > > Hadi > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] printing option
On 11/7/19 12:26 PM, Patel, Lara Anne wrote: Hi Hadi, I have only gotten prints of "stepXXX.pdb" when something is going wrong with the simulation. That is not a printing option but rather supposed to help you in diagnosing the problem. This is indeed their intended purpose. If suppressing them is really necessary, one can do that with export GMX_SUPPRESS_DUMP=1 -Justin From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Hadi Rahmaninejad Sent: Thursday, November 7, 2019 10:04:58 AM To: gmx-us...@gromacs.org Subject: [gmx-users] printing option Hello gromacs users, Can any body give me a reference page in gromacs manual for printing option in energy minimization? I know for nvt other steps, but in energy minimization it automatically prints a lot of "stepXXX.pdb" which are unnecessary and I want to avoid that. Thanks, Hadi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] printing option
Hi Hadi, I have only gotten prints of "stepXXX.pdb" when something is going wrong with the simulation. That is not a printing option but rather supposed to help you in diagnosing the problem. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Hadi Rahmaninejad Sent: Thursday, November 7, 2019 10:04:58 AM To: gmx-us...@gromacs.org Subject: [gmx-users] printing option Hello gromacs users, Can any body give me a reference page in gromacs manual for printing option in energy minimization? I know for nvt other steps, but in energy minimization it automatically prints a lot of "stepXXX.pdb" which are unnecessary and I want to avoid that. Thanks, Hadi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] printing option
Hello gromacs users, Can any body give me a reference page in gromacs manual for printing option in energy minimization? I know for nvt other steps, but in energy minimization it automatically prints a lot of "stepXXX.pdb" which are unnecessary and I want to avoid that. Thanks, Hadi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] polymer & peptide interaction pbc, visualization problem
Hello! I am trying to simulate the adsorption of a certain peptide on a certain polymer surface. For that, I did position restrain of polymer heavy atom and position restrain of protein heavy atoms during the NVT and NPT equilibration and also during energy minimization (EM). The first lines of my minim.mdp file looks like this: ; minim.mdp - used as input into grompp to generate em.tpr define= -DPOSRES -DPP_POSRES integrator= steep; Algorithm (steep = steepest descent minimization) constraints = none The first lines of nvt.mdp and npt.mdp looks like this: define= -DPOSRES -DPP_POSRES; position restrain the protein and polymer ; Run parameters integrator= md; leap-frog integrator nsteps= 10; 2 * 5 = 200 ps dt= 0.002; 1 fs After the equilibration steps, I run my sytem for 100 ns. In my md.mdp file I just include the position restrain of polymer heavy atoms. I also include the position restrain files (posre.itp and posre_polym.itp) in my topology file: ; Include polymer topology #include "amber99sb-ildn.ff/polymer_GMX.itp" ; Include Position restraint file for polymer #ifdef PP_POSRES #include "posre_polym.itp" #endif ; Include water topology #include "./amber99sb-ildn.ff/spce.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 "./amber99sb-ildn.ff/ions.itp" [ system ] ; Name peptide and polymer in water [ molecules ] ; Compound#mols Protein_chain_A 1 Mth 225 SOL 8621 CL 13 I do not get any gmx errors! I remove the pbc with: trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc -mol -center When I first upload my md_0_1.gro file in VMD I can see often “artefacts”. So, a monatomic perpendicular fraction of my layer is over my peptide. And that means of course out of the box. But also in some .gro files, I can see a whole monatomic layer over the peptide! Anyway they disappear once I include my noPBC.xtc file. Once I load my noPBC.xtc file, I saw that the layer is not “stable”. Because when I act out the frames, I see that the layer is shifting over my peptide. It is not the whole layer which is shifting and it is not all the time but in many frames one can see these shifts. I would like to show you some screenshots about this, but the data is too big of one screenshot. I also try this invocation: trjconv -s md.tpr -f md.xtc -o md_noPBC_whole.xtc -pbc whole -center -ur compact trjconv -s md.tpr -f md_noPBC_whole -center -pbc mol But even then, I have the same problem as described before. When I use this: trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc -mol -ur compact I do not see any shifting of my layer. But this time I cannot see any interactions of my peptide with the layer. Can somebody help me with this issue? How can I remove the pbc so I do not have any artefacts of my layer so I can see a adsorption of my peptide? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
I would like to calculate rmsd of protein system, but there is much time taking for trjcat of all simulated trajectories (.trr file) then generated .xtc file by using -center -pbc mol flag. from this .xtc file i use to calculate rms value by using flag g_rms -f .xtc -s .tpr -n .ndx -o .xvg I want to ask here is any other way is available to directly calculate rmsd without using trjcat or less time taking method. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx trjorder
Hi, I would like to calculate the number of ligand molecules within 0.5 nm of a particular amino acid in my protein. I came across the gmx trjorder command (as shown below). gmx trjorder -f Traj.gro -s Traj.tpr -n ProteinLIG.ndx -nshell nshell1.xvg -b 2 -e 4 -na 10 -r 0.5 I have 10 atoms in my ligand. I wanted to ask how accurate is this command in trying to calculate what I want? Akash -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Stochastic Dynamics nsttcouple
Hi John, Thanks for the suggestion! Find a patch here that updates the mdp documentation to clarify the issue you had with nsttcoupl: https://gerrit.gromacs.org/c/gromacs/+/14157 Let me know if things are still unclear. Best, Christian On 11/7/19 1:38 PM, John Whittaker wrote: Hi Justin, Thank you very much for the response. That's the conclusion I kept coming to, but I'm happy to know it for sure now. I'm not sure if others have been confused by this in the past, but it would have saved me some trouble had I known that explicitly from the beginning; any chance this note can be added to the documentation (at least the mdp options page)? Thanks again, John On 11/6/19 10:40 AM, John Whittaker wrote: Hi all, Please correct me if this is the wrong list for this particular question. I have been messing around with the stochastic dynamics integrator in version 5.1 (yes, it's relatively ancient, but I am testing some things involving AdResS) and I can't wrap my head around something: In the src/gromacs/mdlib/update.cpp file, I cannot find a moment when the parameter "nsttcouple" is used in order to determine when the thermostat is applied. I'm not sure if this is a stupid question, but are the friction and noise applied at each step, regardless of the value of nsttcouple? I understand that tcoupl is ignored when the SD integrator is used, but does this mean that nsttcouple is ignored, too? Yes. Formally, the SD integrator does not apply an explicit thermostat algorithm; velocities are updated based on the friction coefficient specified in the .mdp file. nsttcoupl is only relevant when tcoupl is active, which it is not when using SD. -Justin I am by no means an expert in C++ so I could have easily misunderstood or missed something, but this question has been plaguing me for a couple days. Any help I can get to better understand this is much appreciated! Best, John -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Load Imbalance
Hello Shradheya, If you want to enforce dynamic load balancing you can use gmx mdrun -dlb yes instead of the default "auto". However, as I read from the output, your system was not balanced because it was not needed and the overhead of re-distributing atoms might outperform the gain from it. Best, Christian On 11/7/19 12:14 PM, Shradheya R.R. Gupta wrote: Respected Researchers, How to balance the MD simulations? Below is the report. *Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.4%. The balanceable part of the MD step is 70%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.0%.* Thank you Shradheya Gupta DBT-BIF University of Rajasthan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Stochastic Dynamics nsttcouple
Hi Justin, Thank you very much for the response. That's the conclusion I kept coming to, but I'm happy to know it for sure now. I'm not sure if others have been confused by this in the past, but it would have saved me some trouble had I known that explicitly from the beginning; any chance this note can be added to the documentation (at least the mdp options page)? Thanks again, John > > > On 11/6/19 10:40 AM, John Whittaker wrote: >> Hi all, >> >> Please correct me if this is the wrong list for this particular >> question. >> >> I have been messing around with the stochastic dynamics integrator in >> version 5.1 (yes, it's relatively ancient, but I am testing some things >> involving AdResS) and I can't wrap my head around something: >> >> In the src/gromacs/mdlib/update.cpp file, I cannot find a moment when >> the >> parameter "nsttcouple" is used in order to determine when the thermostat >> is applied. I'm not sure if this is a stupid question, but are the >> friction and noise applied at each step, regardless of the value of >> nsttcouple? >> >> I understand that tcoupl is ignored when the SD integrator is used, but >> does this mean that nsttcouple is ignored, too? > > Yes. Formally, the SD integrator does not apply an explicit thermostat > algorithm; velocities are updated based on the friction coefficient > specified in the .mdp file. nsttcoupl is only relevant when tcoupl is > active, which it is not when using SD. > > -Justin > >> I am by no means an expert in C++ so I could have easily misunderstood >> or >> missed something, but this question has been plaguing me for a couple >> days. Any help I can get to better understand this is much appreciated! >> >> Best, >> >> John >> >> >> >> > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Stochastic Dynamics nsttcouple
On 11/6/19 10:40 AM, John Whittaker wrote: Hi all, Please correct me if this is the wrong list for this particular question. I have been messing around with the stochastic dynamics integrator in version 5.1 (yes, it's relatively ancient, but I am testing some things involving AdResS) and I can't wrap my head around something: In the src/gromacs/mdlib/update.cpp file, I cannot find a moment when the parameter "nsttcouple" is used in order to determine when the thermostat is applied. I'm not sure if this is a stupid question, but are the friction and noise applied at each step, regardless of the value of nsttcouple? I understand that tcoupl is ignored when the SD integrator is used, but does this mean that nsttcouple is ignored, too? Yes. Formally, the SD integrator does not apply an explicit thermostat algorithm; velocities are updated based on the friction coefficient specified in the .mdp file. nsttcoupl is only relevant when tcoupl is active, which it is not when using SD. -Justin I am by no means an expert in C++ so I could have easily misunderstood or missed something, but this question has been plaguing me for a couple days. Any help I can get to better understand this is much appreciated! Best, John -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Load Imbalance
Respected Researchers, How to balance the MD simulations? Below is the report. *Dynamic load balancing report: DLB was off during the run due to low measured imbalance. Average load imbalance: 1.4%. The balanceable part of the MD step is 70%, load imbalance is computed from this. Part of the total run time spent waiting due to load imbalance: 1.0%.* Thank you Shradheya Gupta DBT-BIF University of Rajasthan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
