[gmx-users] Peptide-membrane simulation force field parameters
Dear All, I need a suggestion related to simulation of peptide-membrane system. Are CGenFF parameters (from ParamChem) for peptide analogues good enough to couple with Charmm36 parameters for the lipids in a membrane? (provided very low charge and param penalties) Thanks, Tarak -- 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] Problem with 5.0.4 build
Hi, That suggests that your source tree is dirty, somehow. Unpack a fresh tarball and try again. Mark On Tue, Feb 3, 2015 at 2:33 PM, Jim Tuccillo tucci...@sgi.com wrote: Hi Folks, I am seeing the following problem with a 5.0.4 build. I see that others have had this issue also but I haven't seen a solution. Any thoughts on how to address this? Thanks. The build is with the following: cmake .. -DGMX_DOUBLE=ON -DGMX_SIMD=sse4.1 -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DGMX_FFT_LIBRARY=fftw3 -DGMX_PREFER_STATIC_LIBS=YES -DBUILD_SHARED_LIBS=OFF -DFFTW_LIBRARY=$LOCATION/fftw-3.3.3/lib/libfftw3.a -DFFTW_INCLUDE_DIR=$LOCATION/fftw-3.3.3/include where $LOCATION Is specified. CMake Error at src/gromacs/gmxlib/CMakeLists.txt:46 (list): list sub-command REMOVE_ITEM requires two or more arguments. CMake Error at src/gromacs/legacyheaders/CMakeLists.txt:41 (list): list sub-command REMOVE_ITEM requires two or more arguments. CMake Error at src/gromacs/legacyheaders/CMakeLists.txt:42 (list): list sub-command REMOVE_ITEM requires two or more arguments. -- 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] Virtual sites and diffusion coefficients.
Hello Mark, I have tested both models in simulating a variety of properties. The original parametrization results involved predicting the critical point of CO2 and also density at various P and T. I did several NVT simulations to predict density-vs-pressure data. In this case the model with virtual interaction sites gave much better results. In addition to this, simulations performed were performed on pure CO2 at supercritical conditions and mean square displacement was calculated for the CO2 molecule. When compared to the reported ab initio dynamics results the one obtained using virtual sites gave much better agreement. The density of CO2 dissolved in H2O at very dilute concentrations was also studied using both models of CO2 and the results were in good agreement with experimental data for the model with virtual sites. In this case the one without virtual sites also did reasonably well. However, the disparity appears when considering the Measn Square displacement of dilute CO2 solution in water. Here the model without virtual sites is closer to the experimental data. This has become very confusing now. The original parametrization of he model did not involve predicting the transport properties. Also in the published results using the EPM2 model I don't find any mention of the virtual interaction sites. Regards, Sujith. On Tue, Feb 3, 2015 at 1:40 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, With which set of parameters are you able to reproduce the original parametrization results? Mark On Tue, Feb 3, 2015 at 8:04 AM, sujithkakkat . sujithk...@gmail.com wrote: Dear all, I tried simulating the CO2-water mixture with CO2 at a low concentration (0.003 mole fraction) at various temperatures at 1 atmos. I used the EPM2 parameters for the CO2 molecules which includes a flexible OCO angle. I did a separate simulation on the similar system with CO2 model constructed using virtual sites (following Justin Lemkul's tutorial) , with the interaction parameters same as the EPM2 model. In both cases the water model TIP4P was used. I ran 5ns simulation after equilibrium was attained for the T and P values. When plotting the mean square displacement and fitting the graph to get the diffusion coefficients, what I find is that the diffusion coefficient obtained in the case of the CO2 model using virtual sites is much higher (approximately two times) of that obtained for the EPM2 model without the virtual sites. Let me know if any one came across this before. I would like to hear from the more experienced users, what they think about this. I will provide further details on the topology and MD parameters if necessary. Regards, Sujith. -- 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. -- 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] Virtual sites and diffusion coefficients.
Hi, With which set of parameters are you able to reproduce the original parametrization results? Mark On Tue, Feb 3, 2015 at 8:04 AM, sujithkakkat . sujithk...@gmail.com wrote: Dear all, I tried simulating the CO2-water mixture with CO2 at a low concentration (0.003 mole fraction) at various temperatures at 1 atmos. I used the EPM2 parameters for the CO2 molecules which includes a flexible OCO angle. I did a separate simulation on the similar system with CO2 model constructed using virtual sites (following Justin Lemkul's tutorial) , with the interaction parameters same as the EPM2 model. In both cases the water model TIP4P was used. I ran 5ns simulation after equilibrium was attained for the T and P values. When plotting the mean square displacement and fitting the graph to get the diffusion coefficients, what I find is that the diffusion coefficient obtained in the case of the CO2 model using virtual sites is much higher (approximately two times) of that obtained for the EPM2 model without the virtual sites. Let me know if any one came across this before. I would like to hear from the more experienced users, what they think about this. I will provide further details on the topology and MD parameters if necessary. Regards, Sujith. -- 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] Virtual sites and diffusion coefficients.
On 2/3/15 3:56 AM, sujithkakkat . wrote: Hello Mark, I have tested both models in simulating a variety of properties. The original parametrization results involved predicting the critical point of CO2 and also density at various P and T. I did several NVT simulations to predict density-vs-pressure data. In this case the model with virtual interaction sites gave much better results. In addition to this, simulations performed were performed on pure CO2 at supercritical conditions and mean square displacement was calculated for the CO2 molecule. When compared to the reported ab initio dynamics results the one obtained using virtual sites gave much better agreement. The density of CO2 dissolved in H2O at very dilute concentrations was also studied using both models of CO2 and the results were in good agreement with experimental data for the model with virtual sites. In this case the one without virtual sites also did reasonably well. However, the disparity appears when considering the Measn Square displacement of dilute CO2 solution in water. Here the model without virtual sites is closer to the experimental data. This has become very confusing now. The original parametrization of he model did not involve predicting the transport properties. Also in the published results using the EPM2 model I don't find any mention of the virtual interaction sites. I'm rather amazed that my tutorial model works so well, but please note the strong caution I wrote in the topology. There is no validation of this model at all, anywhere in the literature. Any reviewer of your work is going to certainly want an explanation of the parameters, and some model from a tutorial that says it isn't guaranteed to be physically valid probably isn't going to satisfy them. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Problem with 5.0.4 build
Hi Folks, I am seeing the following problem with a 5.0.4 build. I see that others have had this issue also but I haven't seen a solution. Any thoughts on how to address this? Thanks. The build is with the following: cmake .. -DGMX_DOUBLE=ON -DGMX_SIMD=sse4.1 -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DGMX_FFT_LIBRARY=fftw3 -DGMX_PREFER_STATIC_LIBS=YES -DBUILD_SHARED_LIBS=OFF -DFFTW_LIBRARY=$LOCATION/fftw-3.3.3/lib/libfftw3.a -DFFTW_INCLUDE_DIR=$LOCATION/fftw-3.3.3/include where $LOCATION Is specified. CMake Error at src/gromacs/gmxlib/CMakeLists.txt:46 (list): list sub-command REMOVE_ITEM requires two or more arguments. CMake Error at src/gromacs/legacyheaders/CMakeLists.txt:41 (list): list sub-command REMOVE_ITEM requires two or more arguments. CMake Error at src/gromacs/legacyheaders/CMakeLists.txt:42 (list): list sub-command REMOVE_ITEM requires two or more arguments. -- 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] REMD: mdrun_mpi crash with segmentation fault (but mpi is working)
Hi, I trying to learn REMD following the tutorial on gromacs page http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham,_Session_1B on a 4-cores computer. However when I try to use the command: mpirun -np 4 mdrun_mpi -v -multidir equil[0123] (as the tutorial says) the program crashed with the following error: mpirun noticed that process rank 2 with PID 13013 on node debian exited on signal 11 (Segmentation fault). The mpi is running fine with the 4 cores if I run a simple gromacs simulation (NPT equil) in the same machine. So I think it is not a problem of mpi configuration (as I read in another thread) These with gromacs version is 5.0.2 If I try to run the same with an older version of gromacs (4.5.5) the error is different (previously adjusting the options on the mdp file to match changes in syntaxis betweeen versions): [debian:23526] *** An error occurred in MPI_comm_size [debian:23526] *** on communicator MPI_COMM_WORLD [debian:23526] *** MPI_ERR_COMM: invalid communicator [debian:23526] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) But this version also work fine with mpi using the 4 cores on a simple simulation Thanks Bye Felipe Villanelo Lizana Bioquímico Laboratorio de Biología Estructural y Molecular Universidad de Chile -- 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] Problem with Lysozyme in Water Tutorial
On 2/3/15 2:16 PM, Stephen P. Molnar wrote: Ok. I understand the replys. I only have a couple of further questions. A link to grompp is in /usr/local/gromacs/bin. Why isn't ions.mdp in the run directory and then, where is it? You download it from the tutorial site. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/04_ions.html An example .mdp file (the one we will use) can be downloaded here. The word here is a clickable link to download the file. -Justin Thanks in advance. On 02/02/2015 12:29 PM, HANNIBAL LECTER wrote: It just means you either missed grompp -f ions.mdp ... OR the ions.mdp file is not there in the directory where you are performing your simulations. On Mon, Feb 2, 2015 at 12:10 PM, Stephen P. Molnar s.mol...@sbcglobal.net wrote: I have installed v-5.0.4 in Debian Wheezy without any warning or erroe messages. I have tried running the Lysozyme in Water Tutorial ( the one written for v-5) and have generated an error message in Step 4. The message is: File input/output error: ions.mdp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I checked the reference and did not find one [defaults] directive in the .itp file, let alone two Pleas advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and Multivariate www.FoundationForChemistry.com (614)312-7528(c) Skype: smolnar1 -- 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. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Problem with Lysozyme in Water Tutorial
Ok. I understand the replys. I only have a couple of further questions. A link to grompp is in /usr/local/gromacs/bin. Why isn't ions.mdp in the run directory and then, where is it? Thanks in advance. On 02/02/2015 12:29 PM, HANNIBAL LECTER wrote: It just means you either missed grompp -f ions.mdp ... OR the ions.mdp file is not there in the directory where you are performing your simulations. On Mon, Feb 2, 2015 at 12:10 PM, Stephen P. Molnar s.mol...@sbcglobal.net wrote: I have installed v-5.0.4 in Debian Wheezy without any warning or erroe messages. I have tried running the Lysozyme in Water Tutorial ( the one written for v-5) and have generated an error message in Step 4. The message is: File input/output error: ions.mdp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I checked the reference and did not find one [defaults] directive in the .itp file, let alone two Pleas advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and Multivariate www.FoundationForChemistry.com (614)312-7528(c) Skype: smolnar1 -- 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. -- Stephen P. Molnar, Ph.D.Life is a fuzzy set Foundation for ChemistryStochastic and Multivariate www.FoundationForChemistry.com (614)312-7528(c) Skype: smolnar1 -- 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] Using pairs type 2
Hey all, I have been reading many post about this issue, but still do not have a clear answer. I am using the AMBER force-field where 1-4 interactions are scaled (fudgeLJ = 0.5 and fudgeQQ = 0.8333). In addition I use parameters of molecules that require the 1-4 interaction to NOT be scaled. What I did to solve this issue is the follwoing: In the molecules *itp file I listed all 1-4 interactions explicitly. I used the pairs type 2, as in here: [ pairs ] 1 14 2 1 0.161 0.175 0.339967 0.457730 As you can see, I use fudgeQQ=1, with the Real charges, and the needed LJ parameters. I think this works properly, and that it is equivalent (for the molecule of interest) to use type 1 with no explicit parameters (that will be accordingly generated from ffnonbonded.itp), along with a forcefield.itp that sets the fudge factors to 1.0. What worries me is that the manual says type 2 is used for free energy simulations and TI. Can I still use it as mentioned above? Am I missing something? Thanks much, Liel -- 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] Problem with Lysozyme in Water Tutorial
On 02/03/2015 02:30 PM, Justin Lemkul wrote: On 2/3/15 2:16 PM, Stephen P. Molnar wrote: Ok. I understand the replys. I only have a couple of further questions. A link to grompp is in /usr/local/gromacs/bin. Why isn't ions.mdp in the run directory and then, where is it? You download it from the tutorial site. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/04_ions.html An example .mdp file (the one we will use) can be downloaded here. The word here is a clickable link to download the file. -Justin Thanks in advance. On 02/02/2015 12:29 PM, HANNIBAL LECTER wrote: It just means you either missed grompp -f ions.mdp ... OR the ions.mdp file is not there in the directory where you are performing your simulations. On Mon, Feb 2, 2015 at 12:10 PM, Stephen P. Molnar s.mol...@sbcglobal.net wrote: I have installed v-5.0.4 in Debian Wheezy without any warning or erroe messages. I have tried running the Lysozyme in Water Tutorial ( the one written for v-5) and have generated an error message in Step 4. The message is: File input/output error: ions.mdp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I checked the reference and did not find one [defaults] directive in the .itp file, let alone two Pleas advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and Multivariate www.FoundationForChemistry.com (614)312-7528(c) Skype: smolnar1 -- 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. Many thanks flr the reply. It was my fault for not reading carefully enough., -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and Multivariate www.FoundationForChemistry.com (614)312-7528(c) Skype: smolnar1 -- 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] Creating box,
Dear Gromacs User, I am new in Gromacs. I want to create rectangular box like dimensions 5.0 5.0 15.0 and want to put nonane-water-nonane on it. I mean there layers first nonane and water and again nonane layers. Would you please give some idea how to do it. Thank you -- 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] Creating box,
On 2/3/15 8:32 PM, Bishnu Acharya wrote: Dear Gromacs User, I am new in Gromacs. I want to create rectangular box like dimensions 5.0 5.0 15.0 and want to put nonane-water-nonane on it. I mean there layers first nonane and water and again nonane layers. There aren't two nonane layers, because the nonane is continuous via PBC. So really you just have a simple biphasic system. Conveniently, there's a tutorial that illustrates how to do that: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Creating box,
Thank you very much for your suggestion. On Tue, Feb 3, 2015 at 7:35 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/3/15 8:32 PM, Bishnu Acharya wrote: Dear Gromacs User, I am new in Gromacs. I want to create rectangular box like dimensions 5.0 5.0 15.0 and want to put nonane-water-nonane on it. I mean there layers first nonane and water and again nonane layers. There aren't two nonane layers, because the nonane is continuous via PBC. So really you just have a simple biphasic system. Conveniently, there's a tutorial that illustrates how to do that: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/biphasic/index.html -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
