[gmx-users] vdwtype in mdp file for LIE method
hi all freind what is vdwtype in mdp file for LIE method in free energy calculation? best regard -- 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] Umbrella Sampling
Dear Gmx Users, I run SMD to extract the windows for US calculations. The system involves negatively charged ligand and protein. I generated the protein-ligand complex within self assembly MD simulations. I pulled my molecule away and two ions were also detached from the protein surface being attached to my ligand. My question: if I run my US caluclation and combine windows by WHAM (I specified in my umbrella.mdp my ligand as a pull_group1 and same protein residues I pulled it from as pull_group0) will get the PMF profile for my ligand binding or ligand and two ions binding? Steven -- 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] Regarding gromos method in g_cluster
On 2013-07-31 07:20, bipin singh wrote: Hello All, I was trying to do clustering on my MD trajectory using gromos method under g_cluster module. I got one doubt regarding the output, as I used the cutoff of 0.3nm for RMSD calculation, I was expecting that all the snapshots which have RMSD less than or equal to 0.3nm will form the first cluster and the rest of snapshots will form another cluster. But the output gives a single cluster. Please let me know if I have not understood it correctly. It means everything is within 0.3 nm RMSD from each other. Maybe your system is very stable or you did not simulate very long. You can use a shorter cut-off. I am appending the output below: Using gromos method for clustering Using RMSD cutoff 0.3 nm The RMSD ranges from 0.0602553 to 0.411066 nm Average RMSD is 0.107366 Number of structures for matrix 12501 Energy of the matrix is 960.075 nm Found 1 clusters Writing middle structure for each cluster to clusters.pdb Counted 0 transitions in total, max 0 between two specific clusters ## -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Regarding gromos method in g_cluster
Thanks for the reply Prof. David. But in the output it shows that The RMSD ranges from 0.0602553 to 0.411066 nm; this is the point of confusion to me. So I think it should write the snapshots having RMSD greater than 0.3nm (cutoff) to another cluster. On Wed, Jul 31, 2013 at 12:59 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2013-07-31 07:20, bipin singh wrote: Hello All, I was trying to do clustering on my MD trajectory using gromos method under g_cluster module. I got one doubt regarding the output, as I used the cutoff of 0.3nm for RMSD calculation, I was expecting that all the snapshots which have RMSD less than or equal to 0.3nm will form the first cluster and the rest of snapshots will form another cluster. But the output gives a single cluster. Please let me know if I have not understood it correctly. It means everything is within 0.3 nm RMSD from each other. Maybe your system is very stable or you did not simulate very long. You can use a shorter cut-off. I am appending the output below: ##**## Using gromos method for clustering Using RMSD cutoff 0.3 nm The RMSD ranges from 0.0602553 to 0.411066 nm Average RMSD is 0.107366 Number of structures for matrix 12501 Energy of the matrix is 960.075 nm Found 1 clusters Writing middle structure for each cluster to clusters.pdb Counted 0 transitions in total, max 0 between two specific clusters ##** -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 -- *--- Thanks and Regards, Bipin Singh* -- 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] vdwtype in mdp file for LIE method
What does your background reading suggest is a good choice for VDW type? Mark On Wed, Jul 31, 2013 at 9:18 AM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi all freind what is vdwtype in mdp file for LIE method in free energy calculation? best regard -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding gromos method in g_cluster
On 2013-07-31 09:45, bipin singh wrote: Thanks for the reply Prof. David. But in the output it shows that The RMSD ranges from 0.0602553 to 0.411066 nm; this is the point of confusion to me. So I think it should write the snapshots having RMSD greater than 0.3nm (cutoff) to another cluster. I see, then maybe the definition is different (check the source code!). It could be that it is 0.3 nm from the cluster center. On Wed, Jul 31, 2013 at 12:59 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2013-07-31 07:20, bipin singh wrote: Hello All, I was trying to do clustering on my MD trajectory using gromos method under g_cluster module. I got one doubt regarding the output, as I used the cutoff of 0.3nm for RMSD calculation, I was expecting that all the snapshots which have RMSD less than or equal to 0.3nm will form the first cluster and the rest of snapshots will form another cluster. But the output gives a single cluster. Please let me know if I have not understood it correctly. It means everything is within 0.3 nm RMSD from each other. Maybe your system is very stable or you did not simulate very long. You can use a shorter cut-off. I am appending the output below: ##**## Using gromos method for clustering Using RMSD cutoff 0.3 nm The RMSD ranges from 0.0602553 to 0.411066 nm Average RMSD is 0.107366 Number of structures for matrix 12501 Energy of the matrix is 960.075 nm Found 1 clusters Writing middle structure for each cluster to clusters.pdb Counted 0 transitions in total, max 0 between two specific clusters ##** -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Regarding gromos method in g_cluster
Hi Bipin, If A/C have RMSD 0.4 nm, but A/B and B/C both have RMSD 0.3 nm, they'll end up in the same cluster. Cheers, Tsjerk On Wed, Jul 31, 2013 at 9:45 AM, bipin singh bipinel...@gmail.com wrote: Thanks for the reply Prof. David. But in the output it shows that The RMSD ranges from 0.0602553 to 0.411066 nm; this is the point of confusion to me. So I think it should write the snapshots having RMSD greater than 0.3nm (cutoff) to another cluster. On Wed, Jul 31, 2013 at 12:59 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2013-07-31 07:20, bipin singh wrote: Hello All, I was trying to do clustering on my MD trajectory using gromos method under g_cluster module. I got one doubt regarding the output, as I used the cutoff of 0.3nm for RMSD calculation, I was expecting that all the snapshots which have RMSD less than or equal to 0.3nm will form the first cluster and the rest of snapshots will form another cluster. But the output gives a single cluster. Please let me know if I have not understood it correctly. It means everything is within 0.3 nm RMSD from each other. Maybe your system is very stable or you did not simulate very long. You can use a shorter cut-off. I am appending the output below: ##**## Using gromos method for clustering Using RMSD cutoff 0.3 nm The RMSD ranges from 0.0602553 to 0.411066 nm Average RMSD is 0.107366 Number of structures for matrix 12501 Energy of the matrix is 960.075 nm Found 1 clusters Writing middle structure for each cluster to clusters.pdb Counted 0 transitions in total, max 0 between two specific clusters ##** -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://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_Lists http://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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] Regarding gromos method in g_cluster
Now got the point. Thank you Tsjerk Sir and Prof. David for the help. On Wed, Jul 31, 2013 at 1:42 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin, If A/C have RMSD 0.4 nm, but A/B and B/C both have RMSD 0.3 nm, they'll end up in the same cluster. Cheers, Tsjerk On Wed, Jul 31, 2013 at 9:45 AM, bipin singh bipinel...@gmail.com wrote: Thanks for the reply Prof. David. But in the output it shows that The RMSD ranges from 0.0602553 to 0.411066 nm; this is the point of confusion to me. So I think it should write the snapshots having RMSD greater than 0.3nm (cutoff) to another cluster. On Wed, Jul 31, 2013 at 12:59 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2013-07-31 07:20, bipin singh wrote: Hello All, I was trying to do clustering on my MD trajectory using gromos method under g_cluster module. I got one doubt regarding the output, as I used the cutoff of 0.3nm for RMSD calculation, I was expecting that all the snapshots which have RMSD less than or equal to 0.3nm will form the first cluster and the rest of snapshots will form another cluster. But the output gives a single cluster. Please let me know if I have not understood it correctly. It means everything is within 0.3 nm RMSD from each other. Maybe your system is very stable or you did not simulate very long. You can use a shorter cut-off. I am appending the output below: ##**## Using gromos method for clustering Using RMSD cutoff 0.3 nm The RMSD ranges from 0.0602553 to 0.411066 nm Average RMSD is 0.107366 Number of structures for matrix 12501 Energy of the matrix is 960.075 nm Found 1 clusters Writing middle structure for each cluster to clusters.pdb Counted 0 transitions in total, max 0 between two specific clusters ##** -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://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_Lists http://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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 -- *--- Thanks and Regards, Bipin Singh* -- 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] probabilty density of C5-C6 bond of all DNA conformer
Dear Users, I am looking the way to extract the probability density of the C5-C6. I will be very grateful to receive an indication on how to monitor it. Best regards Collins -- 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
Aw: [gmx-users] Umbrella Sampling
will get the PMF profile for my ligand binding or ligand and two ions binding? It would be the ligand and two ions unless the ions also at some point discossiate from the ligand once in solvent. Could add positional restraint for them, but dont know how that effects the calculation? Gesendet:Mittwoch, 31. Juli 2013 um 09:29 Uhr Von:Steven Neumann s.neuman...@gmail.com An:Discussion list for GROMACS users gmx-users@gromacs.org Betreff:[gmx-users] Umbrella Sampling Dear Gmx Users, I run SMD to extract the windows for US calculations. The system involves negatively charged ligand and protein. I generated the protein-ligand complex within self assembly MD simulations. I pulled my molecule away and two ions were also detached from the protein surface being attached to my ligand. My question: if I run my US caluclation and combine windows by WHAM (I specified in my umbrella.mdp my ligand as a pull_group1 and same protein residues I pulled it from as pull_group0) will get the PMF profile for my ligand binding or ligand and two ions binding? Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] topology and coordinate file not matching after grompp
Hello, I have a problem and although I've read almost everything the internet could offer on how differently people have approached this problem, mine hasn't been solved yet. Basically, I am trying to mix 2 different proteins in one box and after doing my grompp to neutralise the system, I get the error number of coordinates in coordinate file (solvated.gro, 85059) does not match topology (topol.top, 85079). This is how my topology file looks: ;GROMACS toplogy ; ;Include the force field #include oplsaa.ff/forcefield.itp ; Include chain topologies #include topol_1AKI.itp #include topol_2CDS.itp ;Include water topology #include spce.itp ;Include generic ion topology #include ions.itp [ system ] Two proteins in water [ molecules ] Protein_1AKI1 Protein_2CDS1 SOL 27053 How can I deduce from this data that the number of coordinates in topol.top is 85079. And what exactly should I do to reduce the number of molecules here so that the 2 files have the same number of coordinates. I will really appreciate the help. I am pretty new with MD simulations Kind Regards, Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Sampling
They do not dissociate...Are you sure? My mdp specifies only ligand as a pull_group1. I think it would change having ions in this group included. On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: will get the PMF profile for my ligand binding or ligand and two ions binding? It would be the ligand and two ions unless the ions also at some point discossiate from the ligand once in solvent. Could add positional restraint for them, but dont know how that effects the calculation? *Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr *Von:* Steven Neumann s.neuman...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* [gmx-users] Umbrella Sampling Dear Gmx Users, I run SMD to extract the windows for US calculations. The system involves negatively charged ligand and protein. I generated the protein-ligand complex within self assembly MD simulations. I pulled my molecule away and two ions were also detached from the protein surface being attached to my ligand. My question: if I run my US caluclation and combine windows by WHAM (I specified in my umbrella.mdp my ligand as a pull_group1 and same protein residues I pulled it from as pull_group0) will get the PMF profile for my ligand binding or ligand and two ions binding? Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Sampling
But even though on the other hand that could be more realistic free energy which could be compare to experiment which also involves ions. Would Justin please comment on this? On Wed, Jul 31, 2013 at 11:46 AM, Steven Neumann s.neuman...@gmail.comwrote: They do not dissociate...Are you sure? My mdp specifies only ligand as a pull_group1. I think it would change having ions in this group included. On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: will get the PMF profile for my ligand binding or ligand and two ions binding? It would be the ligand and two ions unless the ions also at some point discossiate from the ligand once in solvent. Could add positional restraint for them, but dont know how that effects the calculation? *Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr *Von:* Steven Neumann s.neuman...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* [gmx-users] Umbrella Sampling Dear Gmx Users, I run SMD to extract the windows for US calculations. The system involves negatively charged ligand and protein. I generated the protein-ligand complex within self assembly MD simulations. I pulled my molecule away and two ions were also detached from the protein surface being attached to my ligand. My question: if I run my US caluclation and combine windows by WHAM (I specified in my umbrella.mdp my ligand as a pull_group1 and same protein residues I pulled it from as pull_group0) will get the PMF profile for my ligand binding or ligand and two ions binding? Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] umbrella Sampling and PMF- Error estimation
Hi everyone How can we have an error estimation for Gibbs binding free energy when I do umbrella sampling and PMF profile? Actually I did an umbrella sampling for protein and ligand complex and I have a PMF profile now but I do not know how much is my error! Thanks in advance for any suggestion Mohsen -- 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] vdwtype in mdp file for LIE method
On 7/31/13 3:59 AM, Mark Abraham wrote: What does your background reading suggest is a good choice for VDW type? In addition, what does the chosen force field require? -Justin Mark On Wed, Jul 31, 2013 at 9:18 AM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi all freind what is vdwtype in mdp file for LIE method in free energy calculation? best regard -- 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 -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] topology and coordinate file not matching after grompp
On 7/31/13 6:04 AM, chinnu657 wrote: Hello, I have a problem and although I've read almost everything the internet could offer on how differently people have approached this problem, mine hasn't been solved yet. Basically, I am trying to mix 2 different proteins in one box and after doing my grompp to neutralise the system, I get the error number of coordinates in coordinate file (solvated.gro, 85059) does not match topology (topol.top, 85079). This is how my topology file looks: ;GROMACS toplogy ; ;Include the force field #include oplsaa.ff/forcefield.itp ; Include chain topologies #include topol_1AKI.itp #include topol_2CDS.itp ;Include water topology #include spce.itp ;Include generic ion topology #include ions.itp [ system ] Two proteins in water [ molecules ] Protein_1AKI1 Protein_2CDS1 SOL 27053 How can I deduce from this data that the number of coordinates in topol.top is 85079. And what exactly should I do to reduce the number of molecules here so that the 2 files have the same number of coordinates. Number of atoms in Protein_1AKI [moleculetype] + number of atoms in Protein_2CDS [moleculetype] + (3*27053) is the number of atoms that the topology specifies. Cross-check that against the coordinate file. This error always arises for the same reason - incorrect bookkeeping of some sort. You haven't said how you built the system or what commands you gave, for instance, to genbox, so it's hard to be more specific. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] umbrella Sampling and PMF- Error estimation
On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote: Hi everyone How can we have an error estimation for Gibbs binding free energy when I do umbrella sampling and PMF profile? Actually I did an umbrella sampling for protein and ligand complex and I have a PMF profile now but I do not know how much is my error! Read g_wham -h and the associated g_wham paper referenced in the Gromacs manual. It explains everything. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] umbrella Sampling and PMF- Error estimation
Thank you for your reply Dr. Justin On 7/31/13, Justin Lemkul jalem...@vt.edu wrote: On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote: Hi everyone How can we have an error estimation for Gibbs binding free energy when I do umbrella sampling and PMF profile? Actually I did an umbrella sampling for protein and ligand complex and I have a PMF profile now but I do not know how much is my error! Read g_wham -h and the associated g_wham paper referenced in the Gromacs manual. It explains everything. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Sampling
On 7/31/13 6:52 AM, Steven Neumann wrote: But even though on the other hand that could be more realistic free energy which could be compare to experiment which also involves ions. Would Justin please comment on this? I can offer you nothing more than a hand-waving explanation of what I think might happen here, so take that for what it's worth. Since you explicitly asked for my thoughts, such as they are... The dissociation of the ions may be nothing more than an artifact of the pulling conditions. Have you tried different force constants and pull rates to see if this behavior is affected? On Wed, Jul 31, 2013 at 11:46 AM, Steven Neumann s.neuman...@gmail.comwrote: They do not dissociate...Are you sure? My mdp specifies only ligand as a pull_group1. I think it would change having ions in this group included. Even though you're not explicitly pulling the ions, they are being forced to move due to the biasing potential that you are applying. I would think that sufficient sampling in each window (i.e. enough time that you might see dissociation of the ions) would provide you with enough information, but that's hard to predict. My assumption would be that the ions will absolutely impact the free energy of binding, but from what you said above, maybe that's right. Maybe it's not. Only way to find out would be to either exclude the ions or otherwise restrain their initial positions so that you get a clean reaction coordinate involving only the ligand. Then you can decompose the different contributions to the free energy of binding. -Justin On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: will get the PMF profile for my ligand binding or ligand and two ions binding? It would be the ligand and two ions unless the ions also at some point discossiate from the ligand once in solvent. Could add positional restraint for them, but dont know how that effects the calculation? *Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr *Von:* Steven Neumann s.neuman...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* [gmx-users] Umbrella Sampling Dear Gmx Users, I run SMD to extract the windows for US calculations. The system involves negatively charged ligand and protein. I generated the protein-ligand complex within self assembly MD simulations. I pulled my molecule away and two ions were also detached from the protein surface being attached to my ligand. My question: if I run my US caluclation and combine windows by WHAM (I specified in my umbrella.mdp my ligand as a pull_group1 and same protein residues I pulled it from as pull_group0) will get the PMF profile for my ligand binding or ligand and two ions binding? Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Umbrella Sampling
Thank you a lot! On Wed, Jul 31, 2013 at 12:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/31/13 6:52 AM, Steven Neumann wrote: But even though on the other hand that could be more realistic free energy which could be compare to experiment which also involves ions. Would Justin please comment on this? I can offer you nothing more than a hand-waving explanation of what I think might happen here, so take that for what it's worth. Since you explicitly asked for my thoughts, such as they are... The dissociation of the ions may be nothing more than an artifact of the pulling conditions. Have you tried different force constants and pull rates to see if this behavior is affected? On Wed, Jul 31, 2013 at 11:46 AM, Steven Neumann s.neuman...@gmail.com wrote: They do not dissociate...Are you sure? My mdp specifies only ligand as a pull_group1. I think it would change having ions in this group included. Even though you're not explicitly pulling the ions, they are being forced to move due to the biasing potential that you are applying. I would think that sufficient sampling in each window (i.e. enough time that you might see dissociation of the ions) would provide you with enough information, but that's hard to predict. My assumption would be that the ions will absolutely impact the free energy of binding, but from what you said above, maybe that's right. Maybe it's not. Only way to find out would be to either exclude the ions or otherwise restrain their initial positions so that you get a clean reaction coordinate involving only the ligand. Then you can decompose the different contributions to the free energy of binding. -Justin On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: will get the PMF profile for my ligand binding or ligand and two ions binding? It would be the ligand and two ions unless the ions also at some point discossiate from the ligand once in solvent. Could add positional restraint for them, but dont know how that effects the calculation? *Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr *Von:* Steven Neumann s.neuman...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* [gmx-users] Umbrella Sampling Dear Gmx Users, I run SMD to extract the windows for US calculations. The system involves negatively charged ligand and protein. I generated the protein-ligand complex within self assembly MD simulations. I pulled my molecule away and two ions were also detached from the protein surface being attached to my ligand. My question: if I run my US caluclation and combine windows by WHAM (I specified in my umbrella.mdp my ligand as a pull_group1 and same protein residues I pulled it from as pull_group0) will get the PMF profile for my ligand binding or ligand and two ions binding? Steven -- gmx-users mailing list gmx-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-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 -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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 list
Re: [gmx-users] Umbrella Sampling
I am do not want to choose different pulling conditions as I build a model for specific force constant and pulling rate in given force filed. I think restraining would help much more to then exclude the ions impact. Steven On Wed, Jul 31, 2013 at 12:49 PM, Steven Neumann s.neuman...@gmail.comwrote: Thank you a lot! On Wed, Jul 31, 2013 at 12:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/31/13 6:52 AM, Steven Neumann wrote: But even though on the other hand that could be more realistic free energy which could be compare to experiment which also involves ions. Would Justin please comment on this? I can offer you nothing more than a hand-waving explanation of what I think might happen here, so take that for what it's worth. Since you explicitly asked for my thoughts, such as they are... The dissociation of the ions may be nothing more than an artifact of the pulling conditions. Have you tried different force constants and pull rates to see if this behavior is affected? On Wed, Jul 31, 2013 at 11:46 AM, Steven Neumann s.neuman...@gmail.com wrote: They do not dissociate...Are you sure? My mdp specifies only ligand as a pull_group1. I think it would change having ions in this group included. Even though you're not explicitly pulling the ions, they are being forced to move due to the biasing potential that you are applying. I would think that sufficient sampling in each window (i.e. enough time that you might see dissociation of the ions) would provide you with enough information, but that's hard to predict. My assumption would be that the ions will absolutely impact the free energy of binding, but from what you said above, maybe that's right. Maybe it's not. Only way to find out would be to either exclude the ions or otherwise restrain their initial positions so that you get a clean reaction coordinate involving only the ligand. Then you can decompose the different contributions to the free energy of binding. -Justin On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: will get the PMF profile for my ligand binding or ligand and two ions binding? It would be the ligand and two ions unless the ions also at some point discossiate from the ligand once in solvent. Could add positional restraint for them, but dont know how that effects the calculation? *Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr *Von:* Steven Neumann s.neuman...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* [gmx-users] Umbrella Sampling Dear Gmx Users, I run SMD to extract the windows for US calculations. The system involves negatively charged ligand and protein. I generated the protein-ligand complex within self assembly MD simulations. I pulled my molecule away and two ions were also detached from the protein surface being attached to my ligand. My question: if I run my US caluclation and combine windows by WHAM (I specified in my umbrella.mdp my ligand as a pull_group1 and same protein residues I pulled it from as pull_group0) will get the PMF profile for my ligand binding or ligand and two ions binding? Steven -- gmx-users mailing list gmx-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-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 -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- 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/**
[gmx-users] Re: generating user-defined topologies for surfaces
Sorry, still confused here: I have a cell, that is same as residue, contains an inorganic crystal. But since I am creating a surface I have bonds going across periodic boundary, like Al and O shown on the pic? Can I still do it? How do I input it into molecule.rtp? Thank you, V http://gromacs.5086.x6.nabble.com/file/n5010233/Screen_Shot_2013-07-31_at_13.41.17.png -- View this message in context: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-tp5010192p5010233.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Re: generating user-defined topologies for surfaces
On 7/31/13 8:57 AM, Valentina wrote: Sorry, still confused here: I have a cell, that is same as residue, contains an inorganic crystal. But since I am creating a surface I have bonds going across periodic boundary, like Al and O shown on the pic? Can I still do it? How do I input it into molecule.rtp? Construct the bond like you would any other bond. Then set periodic_molecules = yes in the .mdp file. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: generating user-defined topologies for surfaces
perfect! -- View this message in context: http://gromacs.5086.x6.nabble.com/generating-user-defined-topologies-for-surfaces-tp5010192p5010235.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: topology and coordinate file not matching after grompp
Thanks Justin. So, I've understood how to calculate the number of coordinates. That in the topology file matches the amount I calculated (as per how you just taught me). I want to put 2 proteins in the same box. I did this by changing the topology files of the respective proteins to itp. Then a new top file was made in which the itp files were included. I pasted the contents earlier. After this, performed editconf separately on each .gro file and combined them together. then I solvated them. Right before neutralising using genion, while using grompp to get the tpr file is where the error about the mismatch happens. How can I solve this? I've tried making sure my topology file is updated at every stage. Kind Regards, Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010236.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
Fwd: [gmx-users] umbrella Sampling and PMF- Error estimation
Dear Dr.Justin I read that article, It was very helpful. Thanks a lot. After using g_wham with bootstrapping options. I have got an averaged PMF profile (like Fig.2C in that article) and an standard deviation (like Fig.2D In that article) which obtained in this way. As you see, the standard deviation is equal to zero at Z=1.5 nm (because I defined all PMFs as Zero at that point) and it is around 2 kj/mol in Z=0.25 Since I am interested to Gibbs Binding Free Energy(GBFE) (the difference between the Gibbs energy of these points, Z=.0.25 1.5 nm), Is it right to say the error for estimating of GBFE is 2 kj/mol ? Thanks in advance Best On 7/31/13, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Thank you for your reply Dr. Justin On 7/31/13, Justin Lemkul jalem...@vt.edu wrote: On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote: Hi everyone How can we have an error estimation for Gibbs binding free energy when I do umbrella sampling and PMF profile? Actually I did an umbrella sampling for protein and ligand complex and I have a PMF profile now but I do not know how much is my error! Read g_wham -h and the associated g_wham paper referenced in the Gromacs manual. It explains everything. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GROMACS 4.6.3 Static Linking
On Thu, Jul 25, 2013 at 5:55 PM, Mark Abraham mark.j.abra...@gmail.com wrote: That combo is supposed to generate a CMake warning. I also get a warning during linking that some shared library will have to provide some function (getpwuid?) at run time, but the binary is static. That warning has always popped up for me whenever I built static binaries, but it should be harmless unless you run the static binary on a non ABI-compatible library that provides getpwuid(). Andy, have you used the hack which sets the correct link command argument order? http://www.hector.ac.uk/support/documentation/software/gromacs/cmake_static_linking.patch -DGMX_PREFER_STATIC_LIBS=ON will simply instruct CMake to *prefer* static archives when detecting external libraries, the resulting binary will still be dynamically linked against system libraries. Hence, it's strange that this results in broken binaries. What PrgEnv version are you using? Cheers, Szilárd Mark On Thu, Jul 25, 2013 at 4:21 PM, Andrew R Turner a.tur...@epcc.ed.ac.uk wrote: Mark, A bit of testing has revealed that it is the -DGMX_PREFER_STATIC_LIBS=ON flag that makes the difference. With this flag you end up with dynamic executables that do not work (I think due to some glibc problem I have not yet tracked down) whereas if I exclude this option then I get working static executables. Thanks for all your help Andy Quoting Mark Abraham mark.j.abra...@gmail.com on Thu, 25 Jul 2013 14:18:35 +0200: Vitaly has it upside down - it is normally required to build a static binary on Crays. cmake .. -DBUILD_SHARED_LIBS=off just works for building static binaries for me with 4.6.3 on lindgren, a Cray XE6, when using PrgEnv-gnu/4.0.46 Mark On Wed, Jul 24, 2013 at 8:58 AM, Andrew R Turner a.tur...@epcc.ed.ac.uk wrote: Hi Vitaly, Impossible just for v4.6.3? It was certainly possible to create static executables for a Cray XE using v4.6.1 (I know, because I have done it). I followed the same procedure for 4.6.3 and have only managed to get dynamic executables (which do not work) hence my question. I will have more of a dig into the build procedure but just wondered if anyone was aware of anything that has changed between these two minor versions (probably in the build process) that could have precipitated this change in behaviour. Cheers Andy Quoting Dr. Vitaly Chaban vvcha...@gmail.com on Sat, 20 Jul 2013 09:42:41 +0200: Soneone said here that static versions are impossible for Cray... Dr. Vitaly V. Chaban On Fri, Jul 19, 2013 at 12:55 PM, Andrew R Turner a.tur...@epcc.ed.ac.ukwrote: Hi I am having problems creating static versions of the GROMACS binaries for a Cray XE6 (www.hector.ac.uk). The build process I am using is documented at: http://www.hector.ac.uk/**support/documentation/** software/gromacs/compiling_4-**6-1_phase3.phphttp://www.hector.ac.uk/support/documentation/software/gromacs/compiling_4-6-1_phase3.php and successfully produced static binaries for 4.6.1. Has something changed in the new version? In particular, I am setting: -DCMAKE_SKIP_RPATH=YES -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_C_FLAGS=-static -O3 -ftree-vectorize -ffast-math -funroll-loops -DCMAKE_CXX_FLAGS=-static -O3 -ftree-vectorize -ffast-math -funroll-loops but still get dynamic executables: gmx@hector-xe6-5:~/4.6.3-**phase3/bin ldd grompp linux-vdso.so.1 = (0x7fff00da2000) libm.so.6 = /lib64/libm.so.6 (0x7f50dc58f000) libpthread.so.0 = /lib64/libpthread.so.0 (0x7f50dc371000) libAtpSigHandler.so.0 = /opt/cray/lib64/**libAtpSigHandler.so.0 (0x7f50dc16b000) libgfortran.so.3 = /opt/gcc/4.7.2/snos/lib64/**libgfortran.so.3 (0x7f50dbe54000) libscicpp_gnu.so.2 = /opt/cray/lib64/libscicpp_gnu.**so.2 (0x7f50dbc4a000) libsci_gnu_mp.so.2 = /opt/cray/lib64/libsci_gnu_mp.**so.2 (0x7f50d72ec000) libstdc++.so.6 = /opt/gcc/4.7.2/snos/lib64/**libstdc++.so.6 (0x7f50d6fdf000) libfftw3_mpi.so.3 = /opt/cray/lib64/libfftw3_mpi.**so.3 (0x7f50d6dc6000) libfftw3f_mpi.so.3 = /opt/cray/lib64/libfftw3f_mpi.**so.3 (0x7f50d6bae000) libfftw3_threads.so.3 = /opt/cray/lib64/libfftw3_**threads.so.3 (0x7f50d69a6000) libfftw3f_threads.so.3 = /opt/cray/lib64/libfftw3f_**threads.so.3 (0x7f50d679d000) libfftw3.so.3 = /opt/cray/lib64/libfftw3.so.3 (0x7f50d63a2000) libfftw3f.so.3 = /opt/cray/lib64/libfftw3f.so.3 (0x7f50d5f7c000) libmpich_gnu_47.so.1 = /opt/cray/lib64/libmpich_gnu_**47.so.1 (0x7f50d5add000) libmpichf90_gnu_47.so.1 = /opt/cray/lib64/libmpichf90_**gnu_47.so.1 (0x7f50d58da000) libmpl.so.0 = /opt/cray/lib64/libmpl.so.0 (0x7f50d56d5000) librt.so.1 = /lib64/librt.so.1 (0x7f50d54cb000) libxpmem.so.0 = /opt/cray/xpmem/default/lib64/**libxpmem.so.0
[gmx-users] RDF of water
Hello I am trying to calculate the RDF of water with water for a 10 ns MD of pure SPC water simulation (3x3x3 nm box). I run g_rdf with the default -rdf option (atom). The problem is that the integration of the RDF curve up to the first minimum yields a zero value which is obviously not right Do you have any suggestions about this? Should I run g_rdf in a different way? Thanks in advance. Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- 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] Problems with REMD in Gromacs 4.6.3
On Fri, Jul 19, 2013 at 6:59 PM, gigo g...@ibb.waw.pl wrote: Hi! On 2013-07-17 21:08, Mark Abraham wrote: You tried ppn3 (with and without --loadbalance)? I was testing on 8-replicas simulation. 1) Without --loadbalance and -np 8. Excerpts from the script: #PBS -l nodes=8:ppn=3 setenv OMP_NUM_THREADS 4 mpiexec mdrun_mpi -v -cpt 20 -multi 8 -ntomp 4 -replex 2500 -cpi -pin on Excerpts from logs: Using 3 MPI processes Using 4 OpenMP threads per MPI process (...) Overriding thread affinity set outside mdrun_mpi Pinning threads with an auto-selected logical core stride of 1 WARNING: In MPI process #0: Affinity setting for 1/4 threads failed. This can cause performance degradation! If you think your setting are correct, contact the GROMACS developers. WARNING: In MPI process #2: Affinity setting for 4/4 threads failed. Load: The job was allocated 24 cores (3 cores on 8 different nodes). Each OpenMP thread uses ~1/3 of a CPU core on average. Conclusions: MPI runs as many processes as cores requested (nnodes*ppn=24), it ignores OMP_NUM_THREADS env == this is wrong and is not Gromacs issue. Each MPI process forks to 4 threads as requested. The 24-core limit granted by Torque is not violated. 2) The same script, but with -np 8, to limit the number of MPI processes to the number of replicas Logs: Using 1 MPI process Using 4 OpenMP threads (...) Replicas 0,3 and 6: WARNING: Affinity setting for 1/4 threads failed. Replicas 1,2,4,5,7: WARNING: Affinity setting for 4/4 threads failed. Load: The job was allocated 24 cores on 8 nodes. Only on first 3 nodes mpiexec was run. Each OpenMP thread uses ~20% of a CPU core. 3) -np 8 --loadbalance Excerpts from logs: Using 1 MPI process Using 4 OpenMP threads (...) Each replica says: WARNING: Affinity setting for 3/4 threads failed. Load: MPI processes spread evenly on all 8 nodes. Each OpenMP thread uses ~50% of a CPU core. 4) -np 8 --loadbalance, #PBS -l nodes=8:ppn=4 == this worked ~OK with gromacs 4.6.2 Logs: WARNING: Affinity setting for 2/4 threads failed. Load: 32 cores allocated on 8 nodes. MPI processes spread evenly, each OpenMP thread uses ~70% of a CPU core. With 144 replicas the simulation did not produce any results, just got stuck. Some thoughts: the main problem is most probably in the way MPI interprets the information from torque, it is not Gromacs related. MPI ignores OMP_NUM_THREADS. The environment is just broken. Since gromacs-4.6.2 behaved better than 4.6.3 there, I am coming back to it. FYI: unless you are setting thread affinities manually/through the job scheduler, as the mdrun internal affinity setting has a bug in 4.6.2, you are advised to use 4.6.3 (and the better behavior may actually be caused by the non-functional affinity setting). Best, G Mark On Wed, Jul 17, 2013 at 6:30 PM, gigo g...@ibb.waw.pl wrote: On 2013-07-13 11:10, Mark Abraham wrote: On Sat, Jul 13, 2013 at 1:24 AM, gigo g...@ibb.waw.pl wrote: On 2013-07-12 20:00, Mark Abraham wrote: On Fri, Jul 12, 2013 at 4:27 PM, gigo g...@ibb.waw.pl wrote: Hi! On 2013-07-12 11:15, Mark Abraham wrote: What does --loadbalance do? It balances the total number of processes across all allocated nodes. OK, but using it means you are hostage to its assumptions about balance. Thats true, but as long as I do not try to use more resources that the torque gives me, everything is OK. The question is, what is a proper way of running multiple simulations in parallel with MPI that are further parallelized with OpenMP, when pinning fails? I could not find any other. I think pinning fails because you are double-crossing yourself. You do not want 12 MPI processes per node, and that is likely what ppn is setting. AFAIK your setup should work, but I haven't tested it. The thing is that mpiexec does not know that I want each replica to fork to 4 OpenMP threads. Thus, without this option and without affinities (in a sec about it) mpiexec starts too many replicas on some nodes - gromacs complains about the overload then - while some cores on other nodes are not used. It is possible to run my simulation like that: mpiexec mdrun_mpi -v -cpt 20 -multi 144 -replex 2000 -cpi (without --loadbalance for mpiexec and without -ntomp for mdrun) Then each replica runs on 4 MPI processes (I allocate 4 times more cores then replicas and mdrun sees it). The problem is that it is much slower than using OpenMP for each replica. I did not find any other way than --loadbalance in mpiexec and then -multi 144 -ntomp 4 in mdrun to use MPI and OpenMP at the same time on the torque-controlled cluster. That seems highly surprising. I have not yet encountered a job scheduler that was completely lacking a do what I tell you layout scheme. More importantly, why are you using #PBS -l nodes=48:ppn=12? I thing that torque is very similar to all PBS-like
Re: [gmx-users] Re: topology and coordinate file not matching after grompp
On 7/31/13 10:07 AM, chinnu657 wrote: Thanks Justin. So, I've understood how to calculate the number of coordinates. That in the topology file matches the amount I calculated (as per how you just taught me). I want to put 2 proteins in the same box. I did this by changing the topology files of the respective proteins to itp. Then a new top file was made in which the itp files were included. I pasted the contents earlier. After this, performed editconf separately on each .gro file and combined them together. then I solvated them. Right before neutralising using genion, while using grompp to get the tpr file is where the error about the mismatch happens. How can I solve this? I've tried making sure my topology file is updated at every stage. The most common source of problem is water molecules not being accurately accounted for, but the difference cited in the error message is 20, so it's probably not the waters. I can't tell based on the description exactly what you did. As I said before, an exact sequence of commands (copied and pasted from the terminal) is helpful. Concatenating coordinate files is precarious, as you have to conduct manual deletions of lines to fix them after combining them. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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: Fwd: [gmx-users] umbrella Sampling and PMF- Error estimation
On 7/31/13 10:19 AM, Mohsen Ramezanpour wrote: Dear Dr.Justin I read that article, It was very helpful. Thanks a lot. After using g_wham with bootstrapping options. I have got an averaged PMF profile (like Fig.2C in that article) and an standard deviation (like Fig.2D In that article) which obtained in this way. As you see, the standard deviation is equal to zero at Z=1.5 nm (because I defined all PMFs as Zero at that point) and it is around 2 kj/mol in Z=0.25 Since I am interested to Gibbs Binding Free Energy(GBFE) (the difference between the Gibbs energy of these points, Z=.0.25 1.5 nm), Is it right to say the error for estimating of GBFE is 2 kj/mol ? I would suggest you do a bit of reading about propagation of error, and you will have your answer. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] RDF of water
On 7/31/13 10:49 AM, George Patargias wrote: Hello I am trying to calculate the RDF of water with water for a 10 ns MD of pure SPC water simulation (3x3x3 nm box). I run g_rdf with the default -rdf option (atom). The problem is that the integration of the RDF curve up to the first minimum yields a zero value which is obviously not right Do you have any suggestions about this? Should I run g_rdf in a different way? Impossible to tell without seeing the RDF itself. If it doesn't look like Figure 8.3 in the manual, then you've got a problem either with the simulation itself or the way the RDF was calculated. If it does, then you've got a problem with how you're integrating the curve. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: topology and coordinate file not matching after grompp
Hi Justin, Oh, I see. I am going to paste my commands here. pdb2gmx -f 1AKI.pdb -o 1AKI_conf.gro -water spce pdb2gmx -f 2CDS.pdb -o 2CDS_conf.gro -water spce editconf -f 1AKI_conf.gro -o conf1.gro -center 2.5 0 0 editconf -f 2CDS_conf.gro -o conf1.gro -center 7.5 0 0 cat conf1.gro conf2.gro system.gro genconf -f system.gro -o renumber.gro -renumber editconf -f renumber.gro -o newbox.gro -c -d 1.0 -bt dodecahedron genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solvated.gro grompp -f ions.mdp -c solvtaed.gro -p topol.top -o ions.tpr It is after this that I get the error Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010244.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Re: topology and coordinate file not matching after grompp
On 7/31/13 11:29 AM, chinnu657 wrote: Hi Justin, Oh, I see. I am going to paste my commands here. pdb2gmx -f 1AKI.pdb -o 1AKI_conf.gro -water spce pdb2gmx -f 2CDS.pdb -o 2CDS_conf.gro -water spce editconf -f 1AKI_conf.gro -o conf1.gro -center 2.5 0 0 editconf -f 2CDS_conf.gro -o conf1.gro -center 7.5 0 0 cat conf1.gro conf2.gro system.gro genconf -f system.gro -o renumber.gro -renumber editconf -f renumber.gro -o newbox.gro -c -d 1.0 -bt dodecahedron genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solvated.gro grompp -f ions.mdp -c solvtaed.gro -p topol.top -o ions.tpr It is after this that I get the error If you send me renumber.gro and both protein .itp files (off-list), I will have a look and try to figure out where the problem lies. In theory, the above commands should work, provided that the modifications following concatenation were correct, though if genconf didn't complain, whatever you did is probably fine, at least from a syntactical standpoint if not a topological one. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
Aw: Re: [gmx-users] Umbrella Sampling
I did this with a small molecule and the ions were in the solvent, but associated with the ligand, and conversly if the site has a Mg or something etc...it wouldnt be restrained in the normal posres.itp unless you made one for them. It is in the end a matter of view, but I am assuming the change in the binding sites energy would reflect also the ions or the ions being attached to the ligand would not represent a completly solvated ligand (ie energy missing). The positional restraint I stated meant you can just make a two ion -posres_ion and include it in an .mdp however it might screw your system up if your protein is not positionally restrained, or calphas etc...thus I dont know based on your experiment. If the ions move into solution it probably doesnt matter (a quick visual of the simulation). But somone else might have better ideas to help out. Stephan Gesendet:Mittwoch, 31. Juli 2013 um 12:46 Uhr Von:Steven Neumann s.neuman...@gmail.com An:Discussion list for GROMACS users gmx-users@gromacs.org Betreff:Re: [gmx-users] Umbrella Sampling They do not dissociate...Are you sure? My mdp specifies only ligand as a pull_group1. I think it would change having ions in this group included. On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs lloyd.ri...@gmx.ch wrote: will get the PMF profile for my ligand binding or ligand and two ions binding? It would be the ligand and two ions unless the ions also at some point discossiate from the ligand once in solvent. Could add positional restraint for them, but dont know how that effects the calculation? *Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr *Von:* Steven Neumann s.neuman...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* [gmx-users] Umbrella Sampling Dear Gmx Users, I run SMD to extract the windows for US calculations. The system involves negatively charged ligand and protein. I generated the protein-ligand complex within self assembly MD simulations. I pulled my molecule away and two ions were also detached from the protein surface being attached to my ligand. My question: if I run my US caluclation and combine windows by WHAM (I specified in my umbrella.mdp my ligand as a pull_group1 and same protein residues I pulled it from as pull_group0) will get the PMF profile for my ligand binding or ligand and two ions binding? Steven -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: topology and coordinate file not matching after grompp
renumber.gro http://gromacs.5086.x6.nabble.com/file/n5010247/renumber.gro topol_1AKI.itp http://gromacs.5086.x6.nabble.com/file/n5010247/topol_1AKI.itp topol_2CDS.itp http://gromacs.5086.x6.nabble.com/file/n5010247/topol_2CDS.itp I get the feeling you're not going to be able to see the files that I have uploaded here. If you prefer, I can send it to your personal email :) Thank you for your help and the time your putting.. I have attached allt eh files you asked for. Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010247.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Re: topology and coordinate file not matching after grompp
On 7/31/13 11:59 AM, chinnu657 wrote: renumber.gro http://gromacs.5086.x6.nabble.com/file/n5010247/renumber.gro topol_1AKI.itp http://gromacs.5086.x6.nabble.com/file/n5010247/topol_1AKI.itp topol_2CDS.itp http://gromacs.5086.x6.nabble.com/file/n5010247/topol_2CDS.itp I get the feeling you're not going to be able to see the files that I have uploaded here. If you prefer, I can send it to your personal email :) Thank you for your help and the time your putting.. I have attached allt eh files you asked for. You've chopped off part of your protein: 257ARGNH2 3896 8.875 0.492 -2.033 0. 0. 0. 257ARG HH21 3897 8.820 0.535 -1.961 0. 0. 0. 257ARG HH22 3898 8.854 0.511 -2.129 0. 0. 0. 257ARG C 3899 8.936 0.127 -1.437 0. 0. 0. 257ARG O 3900 8.881 0.230 -1.398 0. 0. 0. 8.63000 4.23400 4.31000 There are 129 residues and 1960 atoms in both proteins, thus you should have 3920 atoms total. You have lost the last Leu residue from the second protein, which accounts for your missing atoms. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] RDF of water
Hi Justin Yes, it does look like Fig. 8.3 in the manual if I choose the OW atoms as the the two groups! So there must be a problem with the choice water-water or SOL-SOL for RDF groups. Many thanks! On 7/31/13 10:49 AM, George Patargias wrote: Hello I am trying to calculate the RDF of water with water for a 10 ns MD of pure SPC water simulation (3x3x3 nm box). I run g_rdf with the default -rdf option (atom). The problem is that the integration of the RDF curve up to the first minimum yields a zero value which is obviously not right Do you have any suggestions about this? Should I run g_rdf in a different way? Impossible to tell without seeing the RDF itself. If it doesn't look like Figure 8.3 in the manual, then you've got a problem either with the simulation itself or the way the RDF was calculated. If it does, then you've got a problem with how you're integrating the curve. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- 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] RDF of water
On 7/31/13 12:18 PM, George Patargias wrote: Hi Justin Yes, it does look like Fig. 8.3 in the manual if I choose the OW atoms as the the two groups! So there must be a problem with the choice water-water or SOL-SOL for RDF groups. Indeed there would, because then (with -rdf atom) you're calculating an RDF for all possible atom pairs when choosing whole molecules. -Justin Many thanks! On 7/31/13 10:49 AM, George Patargias wrote: Hello I am trying to calculate the RDF of water with water for a 10 ns MD of pure SPC water simulation (3x3x3 nm box). I run g_rdf with the default -rdf option (atom). The problem is that the integration of the RDF curve up to the first minimum yields a zero value which is obviously not right Do you have any suggestions about this? Should I run g_rdf in a different way? Impossible to tell without seeing the RDF itself. If it doesn't look like Figure 8.3 in the manual, then you've got a problem either with the simulation itself or the way the RDF was calculated. If it does, then you've got a problem with how you're integrating the curve. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Membrane Curvature calaculation
Dear All, How to calculate membrane curvature with function of time in gromacs? what are the parameters that define curvature? mean angle and distance and all ? can anybody help me to solve this problem , because I am new to gromacs..:) Thanks in advance, -- -- 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] Conserved energy (Conserved En.) in NVT simulation
Dear gmx-users, I have run some tests (especially) for pure water, being able to achieve pretty much perfect energy conservation in NVE ensemble (with PME-switch and shifted VDW potential). Then, just for the test, I continued to NVT ensemble by using previous .tpr and .cpt files, but the result was a quite surprise, because there seems to be constant drift in Conserved En.. The drift (100kJ/mol = 0.3%) is not especially large, but it exists with v-rescale temperature coupling. On the other hand, there is no drift at all, if I change to nose-hoover temperature coupling. The behavior is similar also my other systems (liquid mixtures), even though then neither of temperature coupling methods will give exactly perfect conservation, but nose-hoover gives much better one (500 kJ/mol = 3% vs. 60 kJ/mol = 0.4%). Actually, I was expecting to see no drift at all, after all systems behaved fine in NVE ensemble with same parameters with an exception of added temperature coupling (especially when I used double precision for test purpose). So, the main question is, if it is just normal that even such parameters, which give perfect energy conservation in NVE ensemble may introduce drift in Conserved En., when NVT ensemble is used? Or is it just purely (only reason for drift) indication that some temperature coupling methodswork better than others in this sense? Regards, Janne Hirvi-- 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] Expanded ensemble simulation died with fatal error: Something wrong in choosing new lambda state with a Gibbs move
Hi all, I'm running an expanded ensemble simulation using gromacs 4.6.3 and it crashed with the error: Fatal error: Something wrong in choosing new lambda state with a Gibbs move -- probably underflow in weight determination. Denominator is: 0 1.002384e+00 idEnumerator weights 0 -9.1451739502e+02 0.00e+00 0.00e+00 1 -9.128174e+02 0.00e+00 0.00e+00 2 -8.8548516846e+02 0.00e+00 0.00e+00 3 -8.7096899414e+02 0.00e+00 0.00e+00 4 -8.5645288086e+02 0.00e+00 0.00e+00 5 -8.4193676758e+02 0.00e+00 0.00e+00 6 -8.2742059326e+02 0.00e+00 0.00e+00 7 -8.1290447998e+02 0.00e+00 0.00e+00 8 -7.9838836670e+02 0.00e+00 0.00e+00 9 -7.8387219238e+02 0.00e+00 0.00e+00 10 -7.6935607910e+02 0.00e+00 0.00e+00 11 -7.5483990479e+02 0.00e+00 0.00e+00 12 -7.4032379150e+02 0.00e+00 0.00e+00 13 -7.2580767822e+02 0.00e+00 0.00e+00 14 -7.1129150391e+02 0.00e+00 0.00e+00 15 -6.9677539062e+02 0.00e+00 0.00e+00 16 -6.8225927734e+02 0.00e+00 0.00e+00 17 -6.6774316406e+02 0.00e+00 0.00e+00 18 -6.5322698975e+02 0.00e+00 0.00e+00 19 -6.3871087646e+02 0.00e+00 0.00e+00 20 -6.2419470215e+02 0.00e+00 0.00e+00 21 -6.0967858887e+02 0.00e+00 0.00e+00 22 -5.9516247559e+02 0.00e+00 0.00e+00 23 -5.8064630127e+02 0.00e+00 0.00e+00 24 -5.6613018799e+02 0.00e+00 0.00e+00 25 -5.5161407471e+02 0.00e+00 0.00e+00 26 -5.3709790039e+02 0.00e+00 0.00e+00 27 -5.2258178711e+02 0.00e+00 0.00e+00 28 -5.0806564331e+02 0.00e+00 0.00e+00 29 -4.9354953003e+02 0.00e+00 0.00e+00 30 -4.7903335571e+02 0.00e+00 0.00e+00 31 -4.6451724243e+02 0.00e+00 0.00e+00 32 -4.518311e+02 0.00e+00 0.00e+00 33 -4.3548400879e+02 0.00e+00 0.00e+00 34 -4.2096792603e+02 0.00e+00 0.00e+00 35 -4.0645178223e+02 0.00e+00 0.00e+00 36 -3.9193563843e+02 0.00e+00 0.00e+00 37 -3.8107025146e+02 0.00e+00 0.00e+00 38 -3.6290338135e+02 0.00e+00 0.00e+00 39 -3.4838723755e+02 0.00e+00 0.00e+00 40 -3.3387109375e+02 0.00e+00 0.00e+00 41 -3.1935494995e+02 0.00e+00 0.00e+00 42 -3.0483883667e+02 0.00e+00 0.00e+00 43 -2.9032269287e+02 0.00e+00 0.00e+00 44 -2.7580654907e+02 0.00e+00 0.00e+00 45 -2.6129040527e+02 0.00e+00 0.00e+00 46 -2.4677430725e+02 0.00e+00 0.00e+00 47 -2.3225816345e+02 0.00e+00 0.00e+00 48 -2.1774200439e+02 0.00e+00 0.00e+00 49 -2.0322586060e+02 0.00e+00 0.00e+00 50 -1.8970976257e+02 0.00e+00-1.00e+00 51 -1.7419361877e+02 0.00e+00 0.00e+00 52 -1.5967747498e+02 0.00e+00 0.00e+00 53 -1.4516131592e+02 0.00e+00 0.00e+00 54 -1.3064523315e+02 0.00e+00 0.00e+00 55 -1.1612908173e+02 0.00e+00 0.00e+00 56 -1.0161293030e+02 7.0064923216e-45 0.00e+00 57 -8.7096786499e+01 1.4939846888e-38 0.00e+00 58 -7.2580688477e+01 3.0102835162e-32 0.00e+00 59 -5.8064540863e+01 6.0658294505e-26 0.00e+00 60 -4.3548393250e+01 1.865341e-19 0.00e+00 61 -2.9032243729e+01 2.4629560544e-13 0.00e+00 62 -1.5516148567e+01 1.8256696421e-07-1.00e+00 63 0.00e+00 9.976158e-01-1.00e+00 The mdp options for the free energy and expanded ensemble stuff are: free-energy = expanded ; no need to mess with these for now ; sc-alpha = 0 sc-power = 0 sc-r-power = 6 sc-coul = no --- ; Which intermediate state are we simulating? --- init-lambda-state= 0 ; What are the values of lambda at the intermediate states? ;--- ; fep-lambdas = 0.0 0.06667 0.1333 0.2 0.2667 0. 0.4 0.4667 0.5333 0.6 0.6667 0.7333 0.8 0.8667 0.9333 1.0 bonded-lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
[gmx-users] Re: topology and coordinate file not matching after grompp
Thank you very much Justin. It's working fine now :) Really appreciate it. Chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010255.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: topology and coordinate file not matching after grompp
I actually have another problem. When doing my grompp for nvt equilibration, I egt the error, Topology include file posre.itp not found. In my topology file I wrote this: ;Include the force field #include oplsaa.ff/forcefield.itp ; Include chain topologies #include topol_1AKI.itp #include topol_2CDS.itp ; Include Position restraint file #ifdef POSRES #include 1AKI_posre.itp #include 2CDS_posre.itp #endif If the problem is that I need to strictly make it #include posre.itp, then how do I combine the two posre.itp files together? chinnu -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010256.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Re: topology and coordinate file not matching after grompp
On 7/31/13 2:48 PM, chinnu657 wrote: I actually have another problem. When doing my grompp for nvt equilibration, I egt the error, Topology include file posre.itp not found. In my topology file I wrote this: ;Include the force field #include oplsaa.ff/forcefield.itp ; Include chain topologies #include topol_1AKI.itp #include topol_2CDS.itp ; Include Position restraint file #ifdef POSRES #include 1AKI_posre.itp #include 2CDS_posre.itp #endif If the problem is that I need to strictly make it #include posre.itp, then how do I combine the two posre.itp files together? You don't. http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Membrane Curvature calaculation
On 7/31/13 1:38 PM, Nikhil Agrawal wrote: Dear All, How to calculate membrane curvature with function of time in gromacs? what are the parameters that define curvature? mean angle and distance and all ? can anybody help me to solve this problem , because I am new to gromacs..:) Look into the work of Klaus Schulten. He has recently done a lot of membrane curvature stuff and all his papers describe the math in great detail. That will lead you to either auxiliary software that can do the calculations or the information you will need to extract using Gromacs utilities. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Conserved energy (Conserved En.) in NVT simulation
On Wed, Jul 31, 2013 at 7:47 PM, Janne Hirvi janne.hi...@uef.fi wrote: Dear gmx-users, I have run some tests (especially) for pure water, being able to achieve pretty much perfect energy conservation in NVE ensemble (with PME-switch and shifted VDW potential). Great. Then, just for the test, I continued to NVT ensemble by using previous .tpr and .cpt files, but the result was a quite surprise, because there seems to be constant drift in Conserved En.. The drift (100kJ/mol = 0.3%) is not especially large, but it exists with v-rescale temperature coupling. On the other hand, there is no drift at all, if I change to nose-hoover temperature coupling. The behavior is similar also my other systems (liquid mixtures), even though then neither of temperature coupling methods will give exactly perfect conservation, but nose-hoover gives much better one (500 kJ/mol = 3% vs. 60 kJ/mol = 0.4%). Actually, I was expecting to see no drift at all, after all systems behaved fine in NVE ensemble with same parameters with an exception of added temperature coupling (especially when I used double precision for test purpose). So, the main question is, if it is just normal that even such parameters, which give perfect energy conservation in NVE ensemble may introduce drift in Conserved En., when NVT ensemble is used? Or is it just purely (only reason for drift) indication that some temperature coupling methodswork better than others in this sense? In the case of v-rescale, the description of Conserved En. is an overbid. If you see the Bussi 2007 paper, there is a conserved quantity H-tilde, but computing it requires knowledge of the whole of history. IIRC their H is what mdrun reports as Conserved En.. I don't know whether it can be shown that a linear trend in H is equivalent to conservation in H-tilde, but that would be a useful result! Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: topology and coordinate file not matching after grompp
Right, I've understood that now. I've altered all of that. But somehow, the same error message still appears.. -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-and-coordinate-file-not-matching-after-grompp-tp5010221p5010259.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] inconsistent energy drops
Hello, I am performing a MD simulation on a small molecule in a bilayer. The simulation seems to run smoothly but when i graph the energy i see large changes in energy randomly throughout the run(see graph). http://gromacs.5086.x6.nabble.com/file/n5010260/potential_12cc50.png I have looked at each energy term individually and it is the coulomb (SR) which has these large jumps while the rest seem to be normal. Can anyone suggest what might be going on here? (i can add the mdp file if needed) -- View this message in context: http://gromacs.5086.x6.nabble.com/inconsistent-energy-drops-tp5010260.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Conserved energy (Conserved En.) in NVT simulation
Thanks for your comments Mark, If I understood correctly, you are saying, that maybe linear drift in Conserved En. could indicate conservation of that quantity, which we actually should be interested. However, I made meanwhile some additional calculations and noticed that drift in Conserved En. with v-rescale temperature coupling decreases if tau_t is increased. So, in my opinion it would indicate that drift in Conserved En. is more or less related to disturbance due to temperature coupling. If this is true, there shouldn't be drift in perfect case - am I correct? Btw. drifts in my previous mail were per ns. Regards, Janne Dear gmx-users, I have run some tests (especially) for pure water, being able to achieve pretty much perfect energy conservation in NVE ensemble (with PME-switch and shifted VDW potential). Great. Then, just for the test, I continued to NVT ensemble by using previous .tpr and .cpt files, but the result was a quite surprise, because there seems to be constant drift in Conserved En.. The drift (100kJ/mol = 0.3%) is not especially large, but it exists with v-rescale temperature coupling. On the other hand, there is no drift at all, if I change to nose-hoover temperature coupling. The behavior is similar also my other systems (liquid mixtures), even though then neither of temperature coupling methods will give exactly perfect conservation, but nose-hoover gives much better one (500 kJ/mol = 3% vs. 60 kJ/mol = 0.4%). Actually, I was expecting to see no drift at all, after all systems behaved fine in NVE ensemble with same parameters with an exception of added temperature coupling (especially when I used double precision for test purpose). So, the main question is, if it is just normal that even such parameters, which give perfect energy conservation in NVE ensemble may introduce drift in Conserved En., when NVT ensemble is used? Or is it just purely (only reason for drift) indication that some temperature coupling methodswork better than others in this sense? In the case of v-rescale, the description of Conserved En. is an overbid. If you see the Bussi 2007 paper, there is a conserved quantity H-tilde, but computing it requires knowledge of the whole of history. IIRC their H is what mdrun reports as Conserved En.. I don't know whether it can be shown that a linear trend in H is equivalent to conservation in H-tilde, but that would be a useful result! Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: topology and coordinate file not matching after grompp
On 7/31/13 3:10 PM, chinnu657 wrote: Right, I've understood that now. I've altered all of that. But somehow, the same error message still appears.. Without the command issued, exact error message (copied and pasted from the terminal), and relevant topology snippet, there's nothing anyone can do to help aside from telling you whatever you did is still wrong. Please be as explicit as possible to arrive at a conclusion. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] inconsistent energy drops
On 7/31/13 3:38 PM, Brad Van Oosten wrote: Hello, I am performing a MD simulation on a small molecule in a bilayer. The simulation seems to run smoothly but when i graph the energy i see large changes in energy randomly throughout the run(see graph). http://gromacs.5086.x6.nabble.com/file/n5010260/potential_12cc50.png I have looked at each energy term individually and it is the coulomb (SR) which has these large jumps while the rest seem to be normal. Can anyone suggest what might be going on here? (i can add the mdp file if needed) Does visualization of the trajectory indicate anything? The two downward spikes towards the beginning of the run (within 10 ns) should be easy to identify since they stand out very clearly. A binding event or structural change of some sort? Reorientation of lipid headgroups, because of such large dipoles, could play a role here, especially if your small molecule is reacting accordingly. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Interaction energy between specific residue in a set of residues
Dear all, I am looking how I can extract the interaction energy between specific residue in a set of residues. example: I have DT and DA residues, I would like to plot only the energy of the DT. I can extract the DT with the index file, But I am missing information on how to plot the energy base on my index file where I can select only DT. I was only looking the way to extract the c5-c6 distance of adjacent DT without include DA. I will be very grateful to receive any suggestions I wish you all a wonderful day... Collins -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Interaction energy between specific residue in a set of residues
Hi Tomas, I am sorry to come with this further problem of gromacs. I would like to plot an interaction energy between DT without include DA. But I do not know how to ask make g_energy read my index file. Furthermore, I was interested of the distance between C5-C6 in adjacent DT. But I do not know how to ask make_ndx to read C5-C6 in DT with looking for the DA. Please If you can suggest me something it will be great for me. I wish you a wonderful day. Collins On Wed, Jul 31, 2013 at 4:20 PM, Collins Nganou nganoucoll...@gmail.comwrote: Dear all, I am looking how I can extract the interaction energy between specific residue in a set of residues. example: I have DT and DA residues, I would like to plot only the energy of the DT. I can extract the DT with the index file, But I am missing information on how to plot the energy base on my index file where I can select only DT. I was only looking the way to extract the c5-c6 distance of adjacent DT without include DA. I will be very grateful to receive any suggestions I wish you all a wonderful day... Collins -- 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] Interaction energy between specific residue in a set of residues
On 7/31/13 4:20 PM, Collins Nganou wrote: Dear all, I am looking how I can extract the interaction energy between specific residue in a set of residues. Nonbonded energy terms are decomposed using energygrps in the .mdp file along with suitable index groups. example: I have DT and DA residues, I would like to plot only the energy of the DT. I can extract the DT with the index file, But I am missing information on how to plot the energy base on my index file where I can select only DT. You can create index groups for any base or bases you want individually. You haven't shown us what you've done, so it's hard to critique beyond that. I was only looking the way to extract the c5-c6 distance of adjacent DT without include DA. Distances are calculated with g_dist and suitable index groups. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: inconsistent energy drops
looking at the first 2 peaks, they are created from single outlying points in the trajectory. Visually, I can see no discernible difference between it and the frame before/after with the higher energy. -- View this message in context: http://gromacs.5086.x6.nabble.com/inconsistent-energy-drops-tp5010260p5010267.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Expanded ensemble simulation died with fatal error: Something wrong in choosing new lambda state with a Gibbs move
Hi Dejun- The basic problem is that for this particular configuration, the current state is the only state with nonzero weight. Note that the state with the second highest weight has weight 10^-7. When it tries to compare weights in single precision, it has a numerical overflow and fails. A few things: 1. This really should be more robust, so that it will realize it's supposed to stay in the most likely state, since that's the only state with nonzero weight. I have a fix that I've been working on for exactly this problem, but it's not quite ready yet. Hopefully in the next couple of days. 2. This problem is very unlikely to occur in double precision, if you can afford the performance hit in the meantime. 3. If this is a typical average difference, exchanges will be very unlikely. You should probably choose your lambda intervals to be a bit closer together at the end range. Hopefully this will give you enough information to move forward for the time being until a better fix is implemented. On Wed, Jul 31, 2013 at 2:15 PM, Dejun Lin dejun@gmail.com wrote: Hi all, I'm running an expanded ensemble simulation using gromacs 4.6.3 and it crashed with the error: Fatal error: Something wrong in choosing new lambda state with a Gibbs move -- probably underflow in weight determination. Denominator is: 0 1.002384e+00 idEnumerator weights 0 -9.1451739502e+02 0.00e+00 0.00e+00 1 -9.128174e+02 0.00e+00 0.00e+00 2 -8.8548516846e+02 0.00e+00 0.00e+00 3 -8.7096899414e+02 0.00e+00 0.00e+00 4 -8.5645288086e+02 0.00e+00 0.00e+00 5 -8.4193676758e+02 0.00e+00 0.00e+00 6 -8.2742059326e+02 0.00e+00 0.00e+00 7 -8.1290447998e+02 0.00e+00 0.00e+00 8 -7.9838836670e+02 0.00e+00 0.00e+00 9 -7.8387219238e+02 0.00e+00 0.00e+00 10 -7.6935607910e+02 0.00e+00 0.00e+00 11 -7.5483990479e+02 0.00e+00 0.00e+00 12 -7.4032379150e+02 0.00e+00 0.00e+00 13 -7.2580767822e+02 0.00e+00 0.00e+00 14 -7.1129150391e+02 0.00e+00 0.00e+00 15 -6.9677539062e+02 0.00e+00 0.00e+00 16 -6.8225927734e+02 0.00e+00 0.00e+00 17 -6.6774316406e+02 0.00e+00 0.00e+00 18 -6.5322698975e+02 0.00e+00 0.00e+00 19 -6.3871087646e+02 0.00e+00 0.00e+00 20 -6.2419470215e+02 0.00e+00 0.00e+00 21 -6.0967858887e+02 0.00e+00 0.00e+00 22 -5.9516247559e+02 0.00e+00 0.00e+00 23 -5.8064630127e+02 0.00e+00 0.00e+00 24 -5.6613018799e+02 0.00e+00 0.00e+00 25 -5.5161407471e+02 0.00e+00 0.00e+00 26 -5.3709790039e+02 0.00e+00 0.00e+00 27 -5.2258178711e+02 0.00e+00 0.00e+00 28 -5.0806564331e+02 0.00e+00 0.00e+00 29 -4.9354953003e+02 0.00e+00 0.00e+00 30 -4.7903335571e+02 0.00e+00 0.00e+00 31 -4.6451724243e+02 0.00e+00 0.00e+00 32 -4.518311e+02 0.00e+00 0.00e+00 33 -4.3548400879e+02 0.00e+00 0.00e+00 34 -4.2096792603e+02 0.00e+00 0.00e+00 35 -4.0645178223e+02 0.00e+00 0.00e+00 36 -3.9193563843e+02 0.00e+00 0.00e+00 37 -3.8107025146e+02 0.00e+00 0.00e+00 38 -3.6290338135e+02 0.00e+00 0.00e+00 39 -3.4838723755e+02 0.00e+00 0.00e+00 40 -3.3387109375e+02 0.00e+00 0.00e+00 41 -3.1935494995e+02 0.00e+00 0.00e+00 42 -3.0483883667e+02 0.00e+00 0.00e+00 43 -2.9032269287e+02 0.00e+00 0.00e+00 44 -2.7580654907e+02 0.00e+00 0.00e+00 45 -2.6129040527e+02 0.00e+00 0.00e+00 46 -2.4677430725e+02 0.00e+00 0.00e+00 47 -2.3225816345e+02 0.00e+00 0.00e+00 48 -2.1774200439e+02 0.00e+00 0.00e+00 49 -2.0322586060e+02 0.00e+00 0.00e+00 50 -1.8970976257e+02 0.00e+00-1.00e+00 51 -1.7419361877e+02 0.00e+00 0.00e+00 52 -1.5967747498e+02 0.00e+00 0.00e+00 53 -1.4516131592e+02 0.00e+00 0.00e+00 54 -1.3064523315e+02 0.00e+00 0.00e+00 55 -1.1612908173e+02 0.00e+00 0.00e+00 56 -1.0161293030e+02 7.0064923216e-45 0.00e+00 57 -8.7096786499e+01 1.4939846888e-38 0.00e+00 58 -7.2580688477e+01 3.0102835162e-32 0.00e+00 59 -5.8064540863e+01 6.0658294505e-26 0.00e+00 60 -4.3548393250e+01 1.865341e-19 0.00e+00 61 -2.9032243729e+01 2.4629560544e-13 0.00e+00 62 -1.5516148567e+01
[gmx-users] fatal error with charmm/amber forcefield
Dear Gromacs users, I am using gromacs 4.5.4 . Is there any known issue/problem in running hamiltonian replica exchange calculations or FEP with charm27.ff or amber forcefield in gromacs4.5.4 ? I tried running an hamiltonian replica exchange using charmm27.ff by interpolating A state and B state but it gives error that dihedral terms with multiple values can not be interpolated..One need to write all A and B states in topol.top manually. With opls.ff , it does not have any such problem. It works fine... Is it resolved in gromacs 4.6 This is the series error I am getting when using charmm forcefield or amber forcefield: WARNING 1197 [file topol_scale.top, line 2353]: No default Proper Dih. types for perturbed atoms, using normal values ERROR 323 [file topol_scale.top, line 2354]: Cannot automatically perturb a torsion with multiple terms to different form. Please specify perturbed parameters manually for this torsion in your topology! Any idea? Thanks Sanku -- 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] Re: inconsistent energy drops
On 7/31/13 4:45 PM, Brad Van Oosten wrote: looking at the first 2 peaks, they are created from single outlying points in the trajectory. Visually, I can see no discernible difference between it and the frame before/after with the higher energy. To find the source, you'll probably have to further decompose the energy terms using energygrps. Hard to say whether anything is wrong without first figuring out the (potentially) problematic term. It remains entirely possible that what you're seeing is entirely normal, you just have to line up behavior with observation. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Potential Energy Scan
Dear All, Can anyone guide me how to perform the 'potential energy scan' for a dihedral of a small molecule in gromacs? Regrads, Tarak -- 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
