Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD
Hi Justin, I actually did :) but it ended up being bigger than 50 kb so it needed moderator approval to show up. I was hoping it would've been released by now. I'll attach a the details below. Any help/hint is highly appreciated. Reza Details: *1)* Both systems were prepared using VMD membrane package and then waters were removed. I used Gromacs 4.6.1 and NAMD 2.9. *2)* Simulations were run in vacuum as a single-point energy calculations (0 step). PME was not used. *3) *For Gromacs runs, pdb2gmx was used to prepare the system and the output was saved as the pdb format. The mdp file: integrator= md nsteps= 0 nstlog = 1 nstlist= 1 ns_type= grid rlist= 100.0 coulombtype= cut-off rcoulomb= 100.0 rvdw= 100.0 pbc = no *4) *NAMD input file: structure ../0_prep/memb_nowat.psf paratypecharmm on parameterspar_all27_prot_lipid.prm exclude scaled1-4 1-4scaling 1.0 switching off switchdist 8 cutoff 1000 pairlistdist 1000 margin 0 timestep 1.0 outputenergies 1 outputtiming 1 binaryoutput no coordinates ../0_prep/memb_nowat.pdb outputname out dcdfreq 10 temperature 300 run 0 *5)* Energies: For Single POPC (kcal/mol) Gromacs NAMD Diff Bond 43.0022 43.0015 -0.0007 Angle 80.6568 80.6571 0.0003 Dih 29.8083 29.8083 0. Imp 0.8452 0.8452 0. Coul -17.2983 -17.2983 0. LJ -7.0798 -7.0798 0. Pot 129.9343 129.9340 -0.0003 For POPC Memb (kcal/mol) Gromacs NAMD Diff Bond 1539.1181 1539.1162 -0.0019 Angle 3111.9264 3111.9197 -0.0067 Dih 1250.5425 1250.5421 -0.0004 Imp 16.2837 16.2837 0. Coul -1837.8585 -1705.3075 132.5510 LJ -995.0311 -1219.3432 -224.3121 Pot 3084.9904 2993.2110 -91.7794 On Tue, Apr 30, 2013 at 8:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/30/13 4:19 PM, Reza Salari wrote: Hi I have set up two small systems, one with a single POPC lipid, and another system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a similar comparison as in Table 1 in the Par Bjelkmar et al paper (porting charmm ff to gromacs) for my systems. My main question is that for the single POPC, all the potential energy terms match very well, but for the membrane system the non-bonding terms differ significantly. I am providing the full details below and greatly appreciate any hint for better comparison of the energies. Thanks, Reza Salari Details: 1) Both systems were prepared using VMD membrane package: 2) It appears you hit send too early. Please provide the entirety of the details you intended. Complete .mdp files and actual quantification of the differences you are observing are also very important. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD
Hi I have set up two small systems, one with a single POPC lipid, and another system with 23 POPC's arranged as a lipid bilayer. I am hoping to do a similar comparison as in Table 1 in the Par Bjelkmar et al paper (porting charmm ff to gromacs) for my systems. My main question is that for the single POPC, all the potential energy terms match very well, but for the membrane system the non-bonding terms differ significantly. I am providing the full details below and greatly appreciate any hint for better comparison of the energies. Thanks, Reza Salari Details: 1) Both systems were prepared using VMD membrane package: 2) -- 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] New ion parameters and OPLS-AA
Thank you very much Dr Paluch and Dr van der Spoel for your responses. Then it seems it would be safer to use mixing the combination rules as a last resort, although it is comforting to know that other people have used it before successfully. I think I will look for the parameters that are compatible with the OPLS-AA combination rule. Although based on Horinek paper I was sort of hoping that I could convert the parameters for different combination rules. Regards, Reza Salari From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, December 16, 2009 3:10:13 AM Subject: Re: [gmx-users] New ion parameters and OPLS-AA On 12/15/09 11:03 PM, Reza Salari wrote: Thanks for your response. While I will try that (although it seems it needs quite amount of scripting), I remember in the past some people in the mailing list mentioned problems while using nonbond_params directvie with OPLS-AA and in response it was generally suggested to avoid doing this kind of mixing. Like Dr Abraham suggestion here: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? The main thing that I am still unsure about is how the previously mentioned paper converted the sigma values for different combination rules. It seems that there must be a relatively direct way to do this without going through the re-parametrization process. Unfortunately the combination rules are part of the parameterization, simply because changing the combination rules means changing the parameters. Hence I would suggest you look for ion parameters that are compatible with your force field of choice, alternatively a force field that is compatible with your ions of choice. Since these ion parameters were developed by Tom Cheatham I presume that Amber would be a suitable force field. Regards, Reza Salari *From:* Andrew Paluch apal...@nd.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tue, December 15, 2009 4:34:18 PM *Subject:* Re: [gmx-users] New ion parameters and OPLS-AA Read the manual. You can explicitly declare all of your cross terms rather than using the same mixing rule for all terms. You can easily write a script to modify your input files accordingly, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com mailto:resa...@yahoo.com wrote: Hi All, Recently there has been a new set of ion parameters published by Joung and Chetham and I am interested in running some test runs using these parameters. These set of parameters are based on using LB rule (arithmetic mean) for sigmas. However I am using OPLS-AA ff so I am using the combination rule 3 (geometric mean of corresponding A and B values). My question is that can I use the exact sigma values from Cheatham for my simulations? I'm almost positive that I have to change these sigma values to be consistent with the combination rule that I am using. In fact there is a paper by Horinek et al that has a nice table of different ionic sigma and epsilon values from different parameter sets (Aqvist, Jensen, Cheatham,..). The article is here: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes In that table, they have mentioned two sigmas; a usual sigma (which is used with rule 2) and a sigma prime (which can be used with rule 3). However it seems sort of unclear to me how they got these value since in some references that they've mentioned I could find either sigma or sigma prime, not both. So I am guessing there must be some way to convert these two sigmas to each other. So does anyone know if there is such way? Does GROMACS internally treats sigmas as sigma prime for OPLS-AA? I looked at the manual and also searched the mailing list to find an explanation but without luck. I really appreciate any help on clarifying this. Regards, Reza Salari -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala
Re: [gmx-users] New ion parameters and OPLS-AA
Thank you very much. That sounds interesting! BTW, I finally found out that the only way to use parameters developed using different combination rules together, is to define them manually in nonbonding_params section of topology. This sounds a little bit dangerous since it is sort of mixing different approaches. Regards, Reza Salari From: Alexandre Suman de Araujo asara...@if.sc.usp.br To: gmx-users@gromacs.org Sent: Wed, December 16, 2009 11:36:50 AM Subject: Re: [gmx-users] New ion parameters and OPLS-AA If you decide to change the ions parameters, you can use the method described here: http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255DsearchHistoryKey= It is relatively fast and provide nice parameters. Cheers --Alexandre Suman de Araujo Instituto de Física de São Carlos Universidade de São Paulo São Carlos - Brasil Citando Reza Salari resa...@yahoo.com: Thanks for your response. While I will try that (although it seems it needs quite amount of scripting), I remember in the past some people in the mailing list mentioned problems while using nonbond_params directvie with OPLS-AA and in response it was generally suggested to avoid doing this kind of mixing. Like Dr Abraham suggestion here: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? The main thing that I am still unsure about is how the previously mentioned paper converted the sigma values for different combination rules. It seems that there must be a relatively direct way to do this without going through the re-parametrization process. Regards, Reza Salari From: Andrew Paluch apal...@nd.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tue, December 15, 2009 4:34:18 PM Subject: Re: [gmx-users] New ion parameters and OPLS-AA Read the manual. You can explicitly declare all of your cross terms rather than using the same mixing rule for all terms. You can easily write a script to modify your input files accordingly, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com wrote: Hi All, Recently there has been a new set of ion parameters published by Joung and Chetham and I am interested in running some test runs using these parameters. These set of parameters are based on using LB rule (arithmetic mean) for sigmas. However I am using OPLS-AA ff so I am using the combination rule 3 (geometric mean of corresponding A and B values). My question is that can I use the exact sigma values from Cheatham for my simulations? I'm almost positive that I have to change these sigma values to be consistent with the combination rule that I am using. In fact there is a paper by Horinek et al that has a nice table of different ionic sigma and epsilon values from different parameter sets (Aqvist, Jensen, Cheatham,..). The article is here: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes In that table, they have mentioned two sigmas; a usual sigma (which is used with rule 2) and a sigma prime (which can be used with rule 3). However it seems sort of unclear to me how they got these value since in some references that they've mentioned I could find either sigma or sigma prime, not both. So I am guessing there must be some way to convert these two sigmas to each other. So does anyone know if there is such way? Does GROMACS internally treats sigmas as sigma prime for OPLS-AA? I looked at the manual and also searched the mailing list to find an explanation but without luck. I really appreciate any help on clarifying this. Regards, Reza Salari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Novo Webmail IFSC -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send
Re: [gmx-users] New ion parameters and OPLS-AA
Thanks for your response. So basically since the Cheatham parameters are using LB rule, I can never use them with OPLS-AA? I was thinking if I find the parameters for OPLS atoms that are based on geometric rule (if there such a thing exists at all), I could use them along with Cheatham parameters and then define the hetero-atomic LJ parameters in nonbonding_params section. This way I would be mixing parameters that have been developed the same way (regarding combination rules). I understand that one shouldn't directly mix the sigma's that have been developed using different combination rules. If I there is no OPLS parameters based on LB rule, as you mentioned I have to switch to some ff like Amber. Regards, Reza Salari From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, December 16, 2009 1:08:58 PM Subject: Re: [gmx-users] New ion parameters and OPLS-AA Thank you very much. That sounds interesting! BTW, I finally found out that the only way to use parameters developed using different combination rules together, is to define them manually in nonbonding_params section of topology. This sounds a little bit dangerous since it is sort of mixing different approaches. NO don't do that! You will not be using the same parameters, if you change the combination rules. Regards, Reza Salari *From:* Alexandre Suman de Araujo asara...@if.sc.usp.br *To:* gmx-users@gromacs.org *Sent:* Wed, December 16, 2009 11:36:50 AM *Subject:* Re: [gmx-users] New ion parameters and OPLS-AA If you decide to change the ions parameters, you can use the method described here: http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255DsearchHistoryKey http://pubs.acs.org/doi/abs/10.1021/jp064835t?prevSearch=%255Bauthor%253A%2Bde%2BAraujo%255DsearchHistoryKey= It is relatively fast and provide nice parameters. Cheers --Alexandre Suman de Araujo Instituto de Física de São Carlos Universidade de São Paulo São Carlos - Brasil Citando Reza Salari resa...@yahoo.com mailto:resa...@yahoo.com: Thanks for your response. While I will try that (although it seems it needs quite amount of scripting), I remember in the past some people in the mailing list mentioned problems while using nonbond_params directvie with OPLS-AA and in response it was generally suggested to avoid doing this kind of mixing. Like Dr Abraham suggestion here: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? The main thing that I am still unsure about is how the previously mentioned paper converted the sigma values for different combination rules. It seems that there must be a relatively direct way to do this without going through the re-parametrization process. Regards, Reza Salari From: Andrew Paluch apal...@nd.edu mailto:apal...@nd.edu To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Sent: Tue, December 15, 2009 4:34:18 PM Subject: Re: [gmx-users] New ion parameters and OPLS-AA Read the manual. You can explicitly declare all of your cross terms rather than using the same mixing rule for all terms. You can easily write a script to modify your input files accordingly, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com mailto:resa...@yahoo.com wrote: Hi All, Recently there has been a new set of ion parameters published by Joung and Chetham and I am interested in running some test runs using these parameters. These set of parameters are based on using LB rule (arithmetic mean) for sigmas. However I am using OPLS-AA ff so I am using the combination rule 3 (geometric mean of corresponding A and B values). My question is that can I use the exact sigma values from Cheatham for my simulations? I'm almost positive that I have to change these sigma values to be consistent with the combination rule that I am using. In fact there is a paper by Horinek et al that has a nice table of different ionic sigma and epsilon values from different parameter sets (Aqvist, Jensen, Cheatham,..). The article is here: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes In that table, they have mentioned two sigmas; a usual sigma (which is used with rule 2) and a sigma prime (which can be used with rule 3). However it seems sort of unclear to me how they got these value since in some references
[gmx-users] New ion parameters and OPLS-AA
Hi All, Recently there has been a new set of ion parameters published by Joung and Chetham and I am interested in running some test runs using these parameters. These set of parameters are based on using LB rule (arithmetic mean) for sigmas. However I am using OPLS-AA ff so I am using the combination rule 3 (geometric mean of corresponding A and B values). My question is that can I use the exact sigma values from Cheatham for my simulations? I'm almost positive that I have to change these sigma values to be consistent with the combination rule that I am using. In fact there is a paper by Horinek et al that has a nice table of different ionic sigma and epsilon values from different parameter sets (Aqvist, Jensen, Cheatham,..). The article is here: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes In that table, they have mentioned two sigmas; a usual sigma (which is used with rule 2) and a sigma prime (which can be used with rule 3). However it seems sort of unclear to me how they got these value since in some references that they've mentioned I could find either sigma or sigma prime, not both. So I am guessing there must be some way to convert these two sigmas to each other. So does anyone know if there is such way? Does GROMACS internally treats sigmas as sigma prime for OPLS-AA? I looked at the manual and also searched the mailing list to find an explanation but without luck. I really appreciate any help on clarifying this. Regards, Reza Salari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] New ion parameters and OPLS-AA
Thanks for your response. While I will try that (although it seems it needs quite amount of scripting), I remember in the past some people in the mailing list mentioned problems while using nonbond_params directvie with OPLS-AA and in response it was generally suggested to avoid doing this kind of mixing. Like Dr Abraham suggestion here: http://www.mail-archive.com/gmx-users@gromacs.org/msg23147.html Have you tried this kind of mixing for OPLS successfully, without being overridden by the default rules? The main thing that I am still unsure about is how the previously mentioned paper converted the sigma values for different combination rules. It seems that there must be a relatively direct way to do this without going through the re-parametrization process. Regards, Reza Salari From: Andrew Paluch apal...@nd.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tue, December 15, 2009 4:34:18 PM Subject: Re: [gmx-users] New ion parameters and OPLS-AA Read the manual. You can explicitly declare all of your cross terms rather than using the same mixing rule for all terms. You can easily write a script to modify your input files accordingly, Andrew On Tue, Dec 15, 2009 at 4:06 PM, Reza Salari resa...@yahoo.com wrote: Hi All, Recently there has been a new set of ion parameters published by Joung and Chetham and I am interested in running some test runs using these parameters. These set of parameters are based on using LB rule (arithmetic mean) for sigmas. However I am using OPLS-AA ff so I am using the combination rule 3 (geometric mean of corresponding A and B values). My question is that can I use the exact sigma values from Cheatham for my simulations? I'm almost positive that I have to change these sigma values to be consistent with the combination rule that I am using. In fact there is a paper by Horinek et al that has a nice table of different ionic sigma and epsilon values from different parameter sets (Aqvist, Jensen, Cheatham,..). The article is here: http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normalid=JCPSA60001301212450701idtype=cvipsgifs=Yes In that table, they have mentioned two sigmas; a usual sigma (which is used with rule 2) and a sigma prime (which can be used with rule 3). However it seems sort of unclear to me how they got these value since in some references that they've mentioned I could find either sigma or sigma prime, not both. So I am guessing there must be some way to convert these two sigmas to each other. So does anyone know if there is such way? Does GROMACS internally treats sigmas as sigma prime for OPLS-AA? I looked at the manual and also searched the mailing list to find an explanation but without luck. I really appreciate any help on clarifying this. Regards, Reza Salari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Exclusions in topology file seem not working for big systems
Thanks Dr Hess. I didn't get an error message when using grompp, then I think I didn't have too many exclusions. I didn't know about using couple_type in this context before. If I get it correctly, if I want to exclude all non-bonding interactions inside a protein using couple_type, I must define it as follows in each mdp file for each lambda: (I need to decouple all the non-bonding intra molecular interactions for each lambdas): couple_moltype=protein couple_lambda0=none couple_lambda1=none couple-intramol=none If this is right, I will test it for my system which has ~7000 protein atoms. BTW I am still a little confused about the reported 1-4 energies while using exclusions, could you please explain this?. For my smaller system I got zero SR but non-zero 1-4 energies, even that the interactions between all the atoms were excluded. If I remove the pairs in topology file I would get no 1-4 term along with a different dV/dl value. So does it mean if I want to exclude all the intramolecular interactions I have to remove pairs? (my system is frozen and therefore I am not worried about the conformational change of the protein and also I am mainly interested in dV/dl values, which in this case is related to the electrostatic interaction of a residue with water as the charges on that residue being turned off). Regards, Reza Salari From: Berk Hess g...@hotmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, December 3, 2009 3:30:27 AM Subject: RE: [gmx-users] Exclusions in topology file seem not working for big systems Hi, If you really had too many exclusions you would get an error message. So I just tested this. I used the couple_moltype option to couple a 389 atom protein. This generates exclusions between each protein atom and the 388 others. All interactions are excluded correctly (and re-added as special 1-4's because of the couple option). So I don't understand what is going wrong in your case. Berk Date: Wed, 2 Dec 2009 09:31:03 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org Thanks for your response Dr van der Spoel. Then there is a limit on the number of atoms that can be defined in the exclusions section. My smaller system has 60 atoms and I used exclusions successfully for that, so I guess the limit might be a little more than 32. Regarding the use of energygrp_excl,it seems it does not work with PME. If I define the protein in the energygrp_excl group, grompp gives me this warning: Can not exclude the lattice Coulomb energy between energy groups Which I think means some of electrostatics is not going to be excluded between protein atoms. Is there a workaround for this? I think my last resort would be to run a simulation first with PME and without exclusions, and then rerunning it but this time by defining protein in the energygrp_excl and using cut-off instead of PME. Then I guess I will be left with only protein-water interactions. Regards, Reza Salari From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, December 2, 2009 11:59:49 AM Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems Reza Salari wrote: Hi All, I seem to have a hard time to use exclusions in topology file. I have a relatively big system (~400 aa) that I am trying to calculate the difference in desolvation energy (dA) upon turning off charges on a specific residue using thermodynamics integration method. The system is a complex of two proteins and is frozen inside the box (for my project I need it to be frozen).¨ You can have max 32 exclusions per atom AFAIK. However you can use energy_group_excluisions in the mdp file. To calculate the desolvation energy, I need to exclude all the non-bonding interactions among protein atoms, then the dA that I get corresponds to the desolvation energy (and doesn't include the lost interactions between mutated residue and the rest of protein). I couldn't use energygrp_excl in mdp file since I am using PME. So I defined exclusions in topology file as follows (three-dot means that numbers continue to the last number): [ exclusions] 1 2 3 4 5 6 ... 6420 2 1 3 4 5 6 ... 6420 3 1 2 4 5 6 ... 6420 ... ... 6420 1 2 3 ... 6419 I used gmxdump to check that the exclusions were actually implemented, and it seems that they were. However when I use g_energy, I don't get zero energy for short range interactions. Here are the results of g_energy for simulations with and without exclusions: Coul-SR:Protein-Protein LJ-SR:Protein-Protein Coul-14:Protein-Protein LJ-14:Protein-Protein no exclusions-20277.6
Re: [gmx-users] Exclusions in topology file seem not working for big systems
Thank you very much Dr Hess. Then I guess I have to test my rerun workaround that I mentioned for my system. About 1-4 interactions in general, could you a little bit about 1-4 energies while using exclusions please? I hope I am not missing something obvious. The main thing that I am not sure about is if I want to exclude all non-bonding interactions inside a small molecule, do I need to remove [pairs] when adding the [exclusions]? I am using OPLSAA. Regards, Reza Salari From: Berk Hess g...@hotmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, December 3, 2009 12:06:53 PM Subject: RE: [gmx-users] Exclusions in topology file seem not working for big systems Hi, I think that for your problem the couple option is not useful. It does exactly the opposite. I removes all interactions of the selected molecule type with the rest of the system and transform all interactions within the molecule by vacuum non-cutoff LJ and Coulomb interactions. (which end up in special 1-4 energy terms). Berk Date: Thu, 3 Dec 2009 08:59:12 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org Thanks Dr Hess. I didn't get an error message when using grompp, then I think I didn't have too many exclusions. I didn't know about using couple_type in this context before. If I get it correctly, if I want to exclude all non-bonding interactions inside a protein using couple_type, I must define it as follows in each mdp file for each lambda: (I need to decouple all the non-bonding intra molecular interactions for each lambdas): couple_moltype=protein couple_lambda0=none couple_lambda1=none couple-intramol=none If this is right, I will test it for my system which has ~7000 protein atoms. BTW I am still a little confused about the reported 1-4 energies while using exclusions, could you please explain this?. For my smaller system I got zero SR but non-zero 1-4 energies, even that the interactions between all the atoms were excluded. If I remove the pairs in topology file I would get no 1-4 term along with a different dV/dl value. So does it mean if I want to exclude all the intramolecular interactions I have to remove pairs? (my system is frozen and therefore I am not worried about the conformational change of the protein and also I am mainly interested in dV/dl values, which in this case is related to the electrostatic interaction of a residue with water as the charges on that residue being turned off). Regards, Reza Salari From: Berk Hess g...@hotmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, December 3, 2009 3:30:27 AM Subject: RE: [gmx-users] Exclusions in topology file seem not working for big systems Hi, If you really had too many exclusions you would get an error message. So I just tested this. I used the couple_moltype option to couple a 389 atom protein. This generates exclusions between each protein atom and the 388 others. All interactions are excluded correctly (and re-added as special 1-4's because of the couple option). So I don't understand what is going wrong in your case. Berk Date: Wed, 2 Dec 2009 09:31:03 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org Thanks for your response Dr van der Spoel. Then there is a limit on the number of atoms that can be defined in the exclusions section. My smaller system has 60 atoms and I used exclusions successfully for that, so I guess the limit might be a little more than 32. Regarding the use of energygrp_excl,it seems it does not work with PME. If I define the protein in the energygrp_excl group, grompp gives me this warning: Can not exclude the lattice Coulomb energy between energy groups Which I think means some of electrostatics is not going to be excluded between protein atoms. Is there a workaround for this? I think my last resort would be to run a simulation first with PME and without exclusions, and then rerunning it but this time by defining protein in the energygrp_excl and using cut-off instead of PME. Then I guess I will be left with only protein-water interactions. Regards, Reza Salari From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, December 2, 2009 11:59:49 AM Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems Reza Salari wrote: Hi All, I seem to have a hard time to use exclusions in topology file. I have a relatively big system (~400 aa) that I am trying to calculate the difference in desolvation energy (dA) upon turning off charges on a specific residue using thermodynamics
[gmx-users] Different bonding energies for two almost the same systems
Dear Gromacs Users, I've been doing some calculations on methane-methane system in bound and unbound states to see how the energies compare. I set up everything almost the same between two system but I still get different bonding energies for two system. Here is what I did: I first created two methanes separated for 4A to make my bound state. For unbound state, I increased the distance to 10A. The simulations were done in vacuum, all atoms were kept frozen and all non-bonding interactions were excluded (the coulombic and LJ energies are zero). So basically I have two system withe same atoms, bond lengths and angles. In each system, the two methanes don't see each other and are fixed in their positions. However I still get slightly different bonding energies for bound and unbound states. My question is, for this two systems, shouldn't the bonding energies (bond and angle energies) be same? Or more basically, isn't it expected that the potential energies for these two system be same at least for the first step? I hope I am not missing something obvious. I attached mdp, pdb and log files. I also repeated the test with steep algorithm and also md dyanmics but the energies are still different. Thank you in advance, Reza Salari 4_md_md.mdp Description: Binary data bound.pdb Description: Binary data out_bound.log Description: Binary data ubound.pdb Description: Binary data out_unbound.log Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Different bonding energies for two almost the same systems
Thanks Mark for your response. I already did that and the energies are different there too. Actually I think it is reasonable for non-frozen test to have different bonding energies since the potential term is constantly changing but I don't understand why the potentials are different for frozen test? Reza From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wed, November 4, 2009 11:37:32 AM Subject: Re: [gmx-users] Different bonding energies for two almost the same systems Reza Salari wrote: Dear Gromacs Users, I've been doing some calculations on methane-methane system in bound and unbound states to see how the energies compare. I set up everything almost the same between two system but I still get different bonding energies for two system. Here is what I did: I first created two methanes separated for 4A to make my bound state. For unbound state, I increased the distance to 10A. The simulations were done in vacuum, all atoms were kept frozen and all non-bonding interactions were excluded (the coulombic and LJ energies are zero). So basically I have two system withe same atoms, bond lengths and angles. In each system, the two methanes don't see each other and are fixed in their positions. However I still get slightly different bonding energies for bound and unbound states. My question is, for this two systems, shouldn't the bonding energies (bond and angle energies) be same? Or more basically, isn't it expected that the potential energies for these two system be same at least for the first step? I hope I am not missing something obvious. I attached mdp, pdb and log files. I also repeated the test with steep algorithm and also md dyanmics but the energies are still different. Try turning off freeze groups. 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Freezing Algorithm
Hi all, I've got a question regarding freezing algorithm in GROMACS. I appreciate it if somebody explains this. I think in GROMACS 3 for freeze option to work it was generally suggested that all the interactions inside the frozen part should be excluded (either in top or mdp files). However it seems that freeze option works in GROMACS 4 without using any explicit kind of energy exclusions. I am curious to know that if the freezing algorithm has been changed in version 4 to work without exclusions or at the other hand it automatically excludes the interactions in the frozen part. Thanks in advance, Reza Salari___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] A Question About gmxtest
Hi everyone! Thanks to GROMACS developers, version 4.0.4 has been released along with gmxtest 4.0.4. However, I have encountered some problems in passing all tests. I have installed GROMACS on different machines (64 bit AMD and Intel quad cores) using diffrent configure flags (based on instructions in the INSTALL file) and used fftw3 with double and float types, but still tests always fail in COMPLEX (field, tip4p, water) and KERNEL (~16 tests) on all machines. I looked into the test output files and noticed that those failed kernel tests almost always failed in the first step [I think that the test output files only include the steps that failed]. I don't know how much I must be worried about the test results. Has anybody been able to successfully run all tests on a x86_64 machine? If so, could you point out where I could have possibly gone wrong? Thank you in advance,___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Domain Decomposision and Frozen Groups
the nodes Halting parallel program mdrunmpi on CPU 0 out of 8 == The serial version of mdrun works with box 1. I searched the user mailing list and found that some people had similar problem with restraints in the past. I tried to use some -rdd and -dds values, but without any success. Can you please point out where is the source of this error and how I can get domain decomposition and frozen (or restraint) groups to work. Any help or hint is highly appreciated! Reza Salari Express yourself instantly with MSN Messenger! MSN Messenger Express yourself instantly with MSN Messenger! MSN Messenger ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Domain Decomposision and Frozen Groups
Thank you Berk! Actually I need to freeze two proteins so I have to exclude interactions. I already tried to use PME and energygrps_excl together, but grompp used to give me this warning: Can not exclude the lattice Coulomb energy between energy groups which is related to PME (I think it is necessary for me to stick with PME because I mainly want study electrostatic interactions). When I searched the mailng list, some people had suggested that if I want to use PME with frozen groups, I have to use [exclusions] in the topology file. So I did. Any hint for a better workaround? Because I am using a thermodynamic cycle, I am thinking of ignoring this warning... I am trying to understand the domain decomposition method. Indeed I already encountered same error message for small peptides and I figured it out that if I make the box bigger, decomposition would work well. I will try bigger boxes for my proteins, but I have no clear idea about how much bigger the box should be... Thanks From: Berk Hess g...@hotmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, January 22, 2009 4:59:09 PM Subject: RE: [gmx-users] Domain Decomposision and Frozen Groups Hi, The exclusions in the topology introduce long range interactions that require large domain decomposition cells. The md.log of 4.0.3 will tell you this. Remove all those exclusions and add energygrp exclusions in the mdp file. (Or do not use exclusions at all) Berk Date: Thu, 22 Jan 2009 12:37:24 -0800 From: resa...@yahoo.com To: gmx-users@gromacs.org Subject: [gmx-users] Domain Decomposision and Frozen Groups Hi everyone; I am trying to do some simulation using frozen groups on an 8 core computer. I have tow boxes: 1) Box 1 has two proteins and both of them are kept frozen (I used [exclusions] directive in topology file to exclude the interactions in each frozen group, NVT). 2) Box 2 has those two proteins but without being frozen (no use of [exclusions] and freeze options). Here is the mdp file: = integrator = sd dt = 0.002 nsteps = 5 comm_mode = None ns_type = grid pbc = xyz nstlist= 10 rlist = 1 coulombtype = PME rcoulomb = 1 fourierspacing = 0.12 pme_order = 6 ewald_rtol = 1e-6 vdwtype = Switch rvdw_switch = 0.8 rvdw = 0.9 DispCorr = EnerPres nstxout = 500 nstvout = 500 nstlog = 500 nstenergy = 500 nstxtcout= 5000 xtc-precision= 1000 tc_grps = system tau_t= 1 ref_t= 310 energygrps= chainC chainF SOL ; these three lines were commented out for the box 2 simulation freezegrps= chainC chainF freezedim= Y Y Y Y Y Y = I used this command to run the simulations: mpiexec -n 8 mdrunmpi -s eqvspc.tpr -c eqvspc.gro -o eqvspc.trr -x eqvspc.xtc -g eqvspc.log -e eqvspc.edr It works for the box two (no freeze), but for box 1 gives me this error: = Back Off! I just backed up eqvspc.log to ./#eqvspc.log.11# Reading file eqvspc.tpr, VERSION 4.0.3 (single precision) --- Program mdrunmpi, VERSION 4.0.3 Source code file: domdec.c, line: 5858 Fatal error: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 6.25692 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition --- Error on node 0, will try to stop all the nodes Halting parallel program mdrunmpi on CPU 0 out of 8 == The serial version of mdrun works with box 1. I searched the user mailing list and found that some people had similar problem with restraints in the past. I tried to use some -rdd and -dds values, but without any success. Can you please point out where is the source of this error and how I can get domain decomposition and frozen (or restraint) groups to work. Any help or hint is highly appreciated! Reza Salari Express yourself instantly with MSN Messenger! MSN Messenger ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Freezing Groups
Hi everybody, I want to do a simulation using frozen groups and it seems it is much more difficult than I first thought. I searched the mailing list and I still have problems that I can't figure out. It is much appreciated if help me with these problems or point me in the right direction. The scenario is this: I have a protein and a ligand and I want to do free energy calculation. I want to freeze the protein (for a couple of reasons but mainly because it is a big protein and I want to save computation time so I don't want to use restraints) and I know these about freezing the protein (please correct me if any of them is incorrect): -- For minimization, it seems only steep algorithm works. -- I should not use pressure coupling and any constraints (bonds,...) for frozen groups. -- In my mdp file for production run, I defined these: coulombtype=pme energygrps=protein ligand SOL energygrp_excl=protein protein freezegrps=protein freezedim= Y Y Y comm_mode=no -- I know that I should use GROMACS 4.0.2 with fixed freeze code. Now when I want to run the grompp for production mdp, I get this warning: can not exclude the lattice coulomb energy between energy groups I know that this is because I used pme and it seems that I have only two options to solve it: either use other types of long range electrostatics that don't use lattice sum (which I don't want to, because I think PME is much better than others; also I have important electrostatic interactions at protein-ligand interface so I want to use the best method for electrostatics) or use [ exclusions ] part of topology file to exclude interactions of every pair of atoms in the protein (I saw this solution in the mailing this, which is really cumbersome in my case because the protein is big, but I'll do that if I have to). Here are my questions: 1) Isn't there any other solution for this problem? 2) Is that warning really critical? I mean if I am going to compare the two states of the same protein (same protein with different ligands), don't those unexcluded coulomb energies cancel out each other when comparing the total energies of the two states? Or there is no guarantee for this? Thank you in advance. Any kind of help is really appreciated. Reza Salari ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Freezing Groups
Thank you very much Mark for your response. OK, if the [exclusions] way seems reasonable, I'll write the script and test it. I am also curious about knowing something. The manual says that When all non-bonded interactions within or between groups of atoms need to be excluded, is it more convenient and much more efficient to use energy monitor group exclusions. The much more efficient part concerns me a little bit. Because I am looking for efficiency, can you give me an idea about how using energygrp_excl is more efficient than using [exclusions]? Thanks in advance, Reza Salari ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
