Re: [gmx-users] Number of ligand contacts over the trajectories
g_mindist with -on and -d option. On Mon, Oct 14, 2013 at 11:37 AM, anu chandra anu80...@gmail.com wrote: Dear Gromacs users, I am working with protein-ligand interaction. I would like to calculate the number of contacts ligand make with the protein within a specific cut off ( say within 3.5 to 4.5 angstroms), along the simulation trajectories. Is there any Gromacs analysis script, which can help me with doing this calculation? Thanks in advance Regards Anu -- 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] Calculating the distance between protein and ligand during ligand diffusion out of the box
Hello All, I have calculated the distance between the binding pocket of protein and the ligand molecule but due to ligand diffusion out of box, I am getting wrong distance as first it increases till 5nm and then decrease again to around 1nm during the simulation (which is not possible). I have fitted my trajectory with using trjconv -pbc mol -ur compact -center (protein) option. I have also tried the -nojump option but getting the same results for distances. Please suggest how to get the real distance without the PBC effect. -- *--- 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] Calculating the distance between protein and ligand during ligand diffusion out of the box
Thanks for the reply Dr. Justin. I have also thinking of the same possibility but to further confirm, I am sending the link for the plot of the distance between the COM of ligand binding pocket and COM of ligand molecule, please find some time to have a look at the plot and let me know if it seems a feasible behaviour during a simulation. http://researchweb.iiit.ac.in/~bipin.singh/plot.png On Mon, Oct 7, 2013 at 8:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/7/13 10:46 AM, bipin singh wrote: Hello All, I have calculated the distance between the binding pocket of protein and the ligand molecule but due to ligand diffusion out of box, I am getting wrong distance as first it increases till 5nm and then decrease again to around 1nm during the simulation (which is not possible). I have fitted my trajectory with using trjconv -pbc mol -ur compact -center (protein) option. I have also tried the -nojump option but getting the same results for distances. Please suggest how to get the real distance without the PBC effect. It sounds like that very well could be the real distance. If the ligand diffused out, it simply becomes part of the solvent around the protein and can diffuse around freely. -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 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 -- *--- 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] Calculating the distance between protein and ligand during ligand diffusion out of the box
Thanks for the reply Dr. Trayder and Dr. Justin. I have performed unrestrained MD with a ligand bound protein having surface exposed binding pocket (link of the image attached for clarification). I have used a cubic box with vectors 6.432nm and the system size was 4.117 3.878 and 4.059 (in nm). http://researchweb.iiit.ac.in/~bipin.singh/snapshot.png My doubt is how to discriminate between a real ligand binding/unbinding process and the rebinding observed due to PBC effects (i.e. when ligand diffuses out the box and a subsequent another ligand comes and bind from the adjacent periodic image, which may seen as a rebinding event during distance calculation). On Tue, Oct 8, 2013 at 6:37 AM, Trayder Thomas trayder.tho...@monash.eduwrote: With a ligand diffusing as freely as I'm assuming (you've omitted a lot of info, box size etc.) you aren't going to get PBC to play nice, although -nojump should have atleast given you a different wrong answer. Centering the system on the same point you are using to define the binding pocket (may require custom index groups) should get you something more reasonable looking. Also, it depends on the size of your protein and what you're doing but you should consider if it's even relevant whether the ligand is 2nm away or 5? -Trayder On Tue, Oct 8, 2013 at 6:53 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/7/13 1:39 PM, bipin singh wrote: Thanks for the reply Dr. Justin. I have also thinking of the same possibility but to further confirm, I am sending the link for the plot of the distance between the COM of ligand binding pocket and COM of ligand molecule, please find some time to have a look at the plot and let me know if it seems a feasible behaviour during a simulation. http://researchweb.iiit.ac.in/**~bipin.singh/plot.png http://researchweb.iiit.ac.in/~bipin.singh/plot.png Looks like nothing more than random motion to me. Since you haven't told us what you're doing (unrestrained MD? pulling?), it's hard to comment further. -Justin On Mon, Oct 7, 2013 at 8:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/7/13 10:46 AM, bipin singh wrote: Hello All, I have calculated the distance between the binding pocket of protein and the ligand molecule but due to ligand diffusion out of box, I am getting wrong distance as first it increases till 5nm and then decrease again to around 1nm during the simulation (which is not possible). I have fitted my trajectory with using trjconv -pbc mol -ur compact -center (protein) option. I have also tried the -nojump option but getting the same results for distances. Please suggest how to get the real distance without the PBC effect. It sounds like that very well could be the real distance. If the ligand diffused out, it simply becomes part of the solvent around the protein and can diffuse around freely. -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 jalemkul@outerbanks.umaryland.edu 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-users http://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://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/Searchh**ttp://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 http://**www.gromacs.org/Support/**Mailing_Lists 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 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-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http
[gmx-users] Regarding atom numbering in .top and .gro files
Hi all, I want to put off constraint between some bonds in my system based on their atom numbers but the .gro file and .top file atom numbers do not match, because I used .pdb file to generate this .top file using pdb2gmx. (the top files contains the atom numbers based on this initial input .pdb file and the subsequent .gro file contains different atom numbering) I know that grompp generate constraints based on atomtypes in .top file but If I use the .pdb file (used during pdb2gmx) to do this will it be fine, as I will be using this .top file with .gro file for grompp. -- *--- 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] 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] 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] Regarding gromos method in g_cluster
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. 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 ## -- *--- 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] Getting a .tpr file for C-alpha atoms from an all atom .tpr file
Thanks a lot. On Tue, Jul 23, 2013 at 9:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/23/13 11:58 AM, bipin singh wrote: Hello All, I there any way to get a .tpr for C-alpha atoms from an all atom .tpr file. tpbconv -h, particularly point 3. -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 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 -- *--- 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] Getting a .tpr file for C-alpha atoms from an all atom .tpr file
Hello All, I there any way to get a .tpr for C-alpha atoms from an all atom .tpr file. -- *--- 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] g_hbond for trajectory without having box information
According to the suggestion I added the box to the trajectory using -box option of trjconv, using the following commands: trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc then using the g_hbond on the output trjectory (traj_box.xtc) run successfully but gives the wrong number of H-bonds between the proteins atoms. I have also tried to process the output trajectory (traj_box.xtc) with trjconv using -pbc mol -ur compact options before using g_hbond, but again I have got wrong number of H-bonds. Please help me to rectify the error. On Fri, Jul 19, 2013 at 11:19 AM, bipin singh bipinel...@gmail.com wrote: Thanks a lot Prof. David. I will try this. On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2013-07-19 06:26, bipin singh wrote: Hello all, I was using g_hbond to calculate H-bonds for a trajectory made from several individual snapshots from MD simulation, but because this trajectory does not have the coordinates/information for simulation box, g_hbond is giving the following error: Fatal error: Your computational box has shrunk too much. g_hbond_mpi can not handle this situation, sorry. Please let me know, if there is any way to rectify this error. you can add a box to your trajectory using trjconv. -- 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* -- *--- 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] g_hbond for trajectory without having box information
Sorry for my silly mistake. I have a doubt regarding the expected difference in total No. of H-bonds calculated with whole a MD trajectory (protein+solvent box) and H-bonds calculated with concatenated frames (only protein) from a MD trajectory. I mean, will the number of H-bonds present at a particular time in a MD trajectory (protein+solvent), should be exactly same as number of H-bonds calculated using trajectory made of concatenated frames (only protein) from (if we look at number of H-bonds present at same point of time in both). Because I am not getting the exact match between the two, there is random difference of 1-3 H-bonds at some point of time. On Fri, Jul 19, 2013 at 2:43 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/19/13 4:17 AM, bipin singh wrote: According to the suggestion I added the box to the trajectory using -box option of trjconv, using the following commands: trjconv -f traj.xtc -s md.tpr -box 0.9 0.9 0.9 -o traj_box.xtc then using the g_hbond on the output trjectory (traj_box.xtc) run successfully but gives the wrong number of H-bonds between the proteins atoms. I have also tried to process the output trajectory (traj_box.xtc) with trjconv using -pbc mol -ur compact options before using g_hbond, but again I have got wrong number of H-bonds. Please help me to rectify the error. A 0.9-nm cubic box is likely too small to correctly accommodate even an amino acid, let alone an entire protein. -Justin On Fri, Jul 19, 2013 at 11:19 AM, bipin singh bipinel...@gmail.com wrote: Thanks a lot Prof. David. I will try this. On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2013-07-19 06:26, bipin singh wrote: Hello all, I was using g_hbond to calculate H-bonds for a trajectory made from several individual snapshots from MD simulation, but because this trajectory does not have the coordinates/information for simulation box, g_hbond is giving the following error: Fatal error: Your computational box has shrunk too much. g_hbond_mpi can not handle this situation, sorry. Please let me know, if there is any way to rectify this error. you can add a box to your trajectory using trjconv. -- 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 htt**p://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/Searchh**ttp://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 http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- ==** 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 -- *--- 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] g_hbond for trajectory without having box information
Hello all, I was using g_hbond to calculate H-bonds for a trajectory made from several individual snapshots from MD simulation, but because this trajectory does not have the coordinates/information for simulation box, g_hbond is giving the following error: Fatal error: Your computational box has shrunk too much. g_hbond_mpi can not handle this situation, sorry. Please let me know, if there is any way to rectify this error. -- *--- 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] g_hbond for trajectory without having box information
Thanks a lot Prof. David. I will try this. On Fri, Jul 19, 2013 at 10:45 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2013-07-19 06:26, bipin singh wrote: Hello all, I was using g_hbond to calculate H-bonds for a trajectory made from several individual snapshots from MD simulation, but because this trajectory does not have the coordinates/information for simulation box, g_hbond is giving the following error: Fatal error: Your computational box has shrunk too much. g_hbond_mpi can not handle this situation, sorry. Please let me know, if there is any way to rectify this error. you can add a box to your trajectory using trjconv. -- 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] Temperature for individual amino acid residues
Thanks for the reply. I have seen the link. As given in the link that we need to multiply the temperature by (3N-Ncons)/3N. Please let me know if I have correctly interpret context of the statement. N is the total number of protein atoms and Ncons will be equal to total number of constrains. 1) Do we have to take total numbers of pairs mentioned in .top file as a Ncons ( I am using all-bonds constraints in mdp file) ? 2) So, do we need to multiply by this value (single uniform number for all residues) to temperature at each step of every residue in a protein ? On Thu, May 2, 2013 at 4:56 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/2/13 1:54 AM, bipin singh wrote: Hi All, I want to calculate temperature for each individual amino acids residues present in a protein after the simulation. I know that this can be done with help of g_traj, but my concern is whether this will give me correct temperature or not because it was mentioned that g_traj does not mind the constraints. Please let me know what type of correction need to done on the output from g_traj if we need correct temperature values. OR Is there any way to get it from .edr file... http://lists.gromacs.org/**pipermail/gmx-users/2003-**March/004870.htmlhttp://lists.gromacs.org/pipermail/gmx-users/2003-March/004870.html -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- 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] Temperature for individual amino acid residues
Thanks for your reply and suggestions. On Thu, May 2, 2013 at 8:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/2/13 10:28 AM, bipin singh wrote: Thanks for the reply. I have seen the link. As given in the link that we need to multiply the temperature by (3N-Ncons)/3N. Please let me know if I have correctly interpret context of the statement. N is the total number of protein atoms and Ncons will be equal to total number of constrains. N = number of atoms in the group being analyzed Ncons = number of constraints in that same group 1) Do we have to take total numbers of pairs mentioned in .top file as a Ncons ( I am using all-bonds constraints in mdp file) ? Pairs have nothing to do with degrees of freedom. 2) So, do we need to multiply by this value (single uniform number for all residues) to temperature at each step of every residue in a protein ? There is no single value; each group analyzed will have its own scaling factor. Use of the scaling factor depends on what you want to observe, but multiplying each frame's value by a constant and then averaging gives the same as averaging and multiplying by a constant, so you might save yourself some work if you just care about averages. -Justin On Thu, May 2, 2013 at 4:56 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/2/13 1:54 AM, bipin singh wrote: Hi All, I want to calculate temperature for each individual amino acids residues present in a protein after the simulation. I know that this can be done with help of g_traj, but my concern is whether this will give me correct temperature or not because it was mentioned that g_traj does not mind the constraints. Please let me know what type of correction need to done on the output from g_traj if we need correct temperature values. OR Is there any way to get it from .edr file... http://lists.gromacs.org/pipermail/gmx-users/2003- March/004870.htmlhttp://lists.gromacs.org/**pipermail/gmx-users/2003-**March/004870.html http://**lists.gromacs.org/pipermail/**gmx-users/2003-March/004870.** htmlhttp://lists.gromacs.org/pipermail/gmx-users/2003-March/004870.html -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://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/Searchh**ttp://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 http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- 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] Temperature for individual amino acid residues
Hi All, I want to calculate temperature for each individual amino acids residues present in a protein after the simulation. I know that this can be done with help of g_traj, but my concern is whether this will give me correct temperature or not because it was mentioned that g_traj does not mind the constraints. Please let me know what type of correction need to done on the output from g_traj if we need correct temperature values. OR Is there any way to get it from .edr file... -- *--- 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] Doubt about the Gromacs versions
Thanks for the clarification. On Thu, Apr 25, 2013 at 7:48 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/25/13 9:48 AM, Richard Broadbent wrote: The 4.6.1 release is a more advanced version of gromacs with the latest kernels and features (GPU support, verlet cut-offs etc.). 4.5.7 is a maintenance release for those of us who for whatever reason wish to keep using the older 4.5.x series release. It mainly adds fixes made to the 4.6.x series to the 4.5.x version of the code. I use it as most of my calculations were conducted in 4.5.5 so this version allows me to use exactly the same setup as I was using before. If you are starting a new project I would suggest that the 4.6.x series is what you should use as it is substantially faster (for a system I'm running that contains no water on an Intel sandy-bridge system it is more than 50% faster). This series will also probably receive more attention in terms of bug fixes and new releases (though I'm not a developer so I could be wrong about that). Quite right. 4.5.7 is expected to be the last version in the 4.5.x series, and I suspect that will be true unless we discover some catastrophic bug that needs to be patched in older versions. 4.6.x (and the eventual transition to 5.0) will receive the greatest amount of attention from here on out. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- 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] Doubt about the Gromacs versions
Thanks for your reply. On Thu, Apr 25, 2013 at 7:18 PM, Richard Broadbent richard.broadben...@imperial.ac.uk wrote: The 4.6.1 release is a more advanced version of gromacs with the latest kernels and features (GPU support, verlet cut-offs etc.). 4.5.7 is a maintenance release for those of us who for whatever reason wish to keep using the older 4.5.x series release. It mainly adds fixes made to the 4.6.x series to the 4.5.x version of the code. I use it as most of my calculations were conducted in 4.5.5 so this version allows me to use exactly the same setup as I was using before. If you are starting a new project I would suggest that the 4.6.x series is what you should use as it is substantially faster (for a system I'm running that contains no water on an Intel sandy-bridge system it is more than 50% faster). This series will also probably receive more attention in terms of bug fixes and new releases (though I'm not a developer so I could be wrong about that). Richard On 25/04/13 14:39, bipin singh wrote: Hi, Please let me know which one is the recent version of gromacs (with latest bugfixes) among the below. 4.5.7 and 4.6.1 And what is the reason behind the update for 4.5.x versions if 4.6.x versions are already available. -- 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] RMSD from the average structure
Dear Sir, Thanks for the useful insight. On Fri, Apr 26, 2013 at 2:21 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Average coordinates are problematic and not generally representative. Consider for instance the average coordinates of a methyl group connected to X. The rotation around the C-X bond causes the average positions of the hydrogens to line up. Consider using g_cluster to find representative structures from your trajectory. Erik On 26 Apr 2013, at 06:59, bipin singh bipinel...@gmail.com wrote: Thanks for your reply. Actually I am interested to see how much structural deviation is occurring in a protein during the simulation from its average position of atoms rather than the initial position (crystal structure or starting structure). The motivation of doing this analysis is the fact that in real solution phase, a system may not be static and if we consider the time average structure of a simulation to be the real representative of the structure in solution phase rather than static crystal structure. On Fri, Apr 26, 2013 at 2:06 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin Singh, That indeed gives you the RMSD against the average. Do think about it a bit more: do you want the average of the whole structure, or should you account for a phase of relaxation? Cheers, Tsjerk On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/24/13 3:06 AM, bipin singh wrote: Hi all, Please let me know whether this is the right way to calculate RMSD from the average structure from a simulation: g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg average.pdb: is the pdb file produced using -ox option of g_rmsf. You can calculate RMSD with respect to whatever structure you like, but the interpretation and justification for doing so are up to you. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- 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 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] Doubt about the Gromacs versions
Hi, Please let me know which one is the recent version of gromacs (with latest bugfixes) among the below. 4.5.7 and 4.6.1 And what is the reason behind the update for 4.5.x versions if 4.6.x versions are already available. -- *--- 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] RMSD from the average structure
Thanks for your reply. Actually I am interested to see how much structural deviation is occurring in a protein during the simulation from its average position of atoms rather than the initial position (crystal structure or starting structure). The motivation of doing this analysis is the fact that in real solution phase, a system may not be static and if we consider the time average structure of a simulation to be the real representative of the structure in solution phase rather than static crystal structure. On Fri, Apr 26, 2013 at 2:06 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin Singh, That indeed gives you the RMSD against the average. Do think about it a bit more: do you want the average of the whole structure, or should you account for a phase of relaxation? Cheers, Tsjerk On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/24/13 3:06 AM, bipin singh wrote: Hi all, Please let me know whether this is the right way to calculate RMSD from the average structure from a simulation: g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg average.pdb: is the pdb file produced using -ox option of g_rmsf. You can calculate RMSD with respect to whatever structure you like, but the interpretation and justification for doing so are up to you. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- 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] RMSD from the average structure
Hi all, Please let me know whether this is the right way to calculate RMSD from the average structure from a simulation: g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg average.pdb: is the pdb file produced using -ox option of g_rmsf. -- *--- 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] Re: Salt bridge Calculations
You can use g_dist with specific atoms indices to calculate distances, if you already have the information about atoms involved in salt bridge interactions. On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Kindly clarify my doubt regarding salt bridge calculation. Thank you Regards Kavya On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M hmkv...@gmail.com wrote: Dear users, For calculating salt bridge in proteins I am using g_hbond instead of g_saltbr. In g_hbond I use contact and mention two indices consisting of group 1: ASP_GLU__OD1_OD2_OE1_OE2: group 2: ARG_LYS__NZ_NE_NH1_NH2: I use the command: g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx -contact -r 0.4 -hbm matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5 Is this approach correct? Thank you Kavya -- 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
Re: [gmx-users] Free energy landscape by g_sham
g_sham calculates free energy landscapes by computing the joint probability distribution from the two dimensional plane constructed using two quantities (in your case it will be rmsd and radius of gyration). Conformations sampled during the simulation were projected on this two dimensional plane, and the number of points occupied by each cell was counted. The grid cell containing the maximum number of points is then assigned as the reference cell, with a free energy value of zero. Free energies for all the other cells were assigned with respect to this reference cell using the following equation: ΔG = -kbT ln P(x,y)/Pmin P(x,y) is the estimate of probability density function obtained from a histogram of MD data and Pmin is the maximum of the probability density function. Kb is the Boltzmann constant, and T is the temperature corresponding to each simulation. On Sun, Mar 31, 2013 at 10:35 AM, Kavyashree M hmkv...@gmail.com wrote: Dear users, Can someone kindly explain how g_sham calculates the free energy landscape of given two quantities say, rmsd and radius of gyration. Any references are welcome. Thank you with Regards Kavya -- 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] Difference in Number of contacts through g_hbond and g_mindist
Hi All, I have a doubt regarding the calculation of number of contacts between two groups. Because, I am getting different number of contacts calculated through g_hbond -contact option and g_mindist -on option. I have used same cutoff for distance (0.6nm) in both the cases. -- *--- 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] Difference in Number of contacts through g_hbond and g_mindist
Thanks for the reply. The difference is almost double, through g_hbond the average number of contacts are 1821 and through g_mindist it is 3643. The calculation group does not contains hydrogen atoms. On Mon, Mar 4, 2013 at 8:14 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/13 9:08 AM, bipin singh wrote: Hi All, I have a doubt regarding the calculation of number of contacts between two groups. Because, I am getting different number of contacts calculated through g_hbond -contact option and g_mindist -on option. I have used same cutoff for distance (0.6nm) in both the cases. How different are the results? The g_hbond code is very complex, but you'd probably have to go into the inner workings of both programs to understand why. I also do not know whether other settings in g_hbond will matter, like -merge, or whether or not g_hbond will only calculate contacts among H-bond participating groups. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- 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] Difference in Number of contacts through g_hbond and g_mindist
Thanks a lot for the suggestions. It worked. On Mon, Mar 4, 2013 at 8:44 PM, Erik Marklund er...@xray.bmc.uu.se wrote: As Justin implied, -merge could potentially make a factor of 2. Try g_hbond -nomerge. Erik On Mar 4, 2013, at 4:02 PM, bipin singh wrote: Thanks for the reply. The difference is almost double, through g_hbond the average number of contacts are 1821 and through g_mindist it is 3643. The calculation group does not contains hydrogen atoms. On Mon, Mar 4, 2013 at 8:14 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/4/13 9:08 AM, bipin singh wrote: Hi All, I have a doubt regarding the calculation of number of contacts between two groups. Because, I am getting different number of contacts calculated through g_hbond -contact option and g_mindist -on option. I have used same cutoff for distance (0.6nm) in both the cases. How different are the results? The g_hbond code is very complex, but you'd probably have to go into the inner workings of both programs to understand why. I also do not know whether other settings in g_hbond will matter, like -merge, or whether or not g_hbond will only calculate contacts among H-bond participating groups. -Justin -- ==== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://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/Searchh**ttp://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 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-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 thewww 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
[gmx-users] MDP settings for No Temperature Coupling
Hello All, I want to know how to mention a group (group2) without any temperature coupling in mdp file. From the manual I got to know that we should mention tau_t= -1 for no temperature coupling. And in the ref_temp section I have mention two values, 300K for coupled part (group1) and 10k for uncoupled part (group2). But my doubt is while generating velocities, which temperature I should mention in gen_temp section (i.e. 300K or 10K), because as far as I know we can not mention two different temperatures in gen_temp section while generating velocities. But ideally I want the uncoupled part to be at 10K and coupled part at 300K at the starting. Please let me know, which of the below scheme is correct for this purpose: * Method:1* Tcoupl= V-rescale tau_t= 0.1 -1 tc_grps= group1 group2 ref_t= 300 10 gen_vel= yes gen_temp= 300 *Method:2* Tcoupl= V-rescale tau_t= 0.1 -1 tc_grps= group1 group2 ref_t= 300 10 gen_vel= yes gen_temp= 10 -- *--- 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] Reference structure for PCA.
Hi vivek, I have few questions related to your query: During covariance matrix calculation, g_covar by default takes average structure of the trajectory as a reference structure then why you are giving it average structure of your trajectory (0-100ns) manually. Moreover without looking at your commands which you have used, it would be difficult for anyone that why are you getting these surprising results. On Thu, Feb 7, 2013 at 1:26 PM, vivek modi modi.vivek2...@gmail.com wrote: Hello, I have troubled you with a similar question before also, but I guess I need some more clarification. My question is about the reference structure in PCA analysis. I have 100ns long protein simulation which I want to analyze using PCA. The RMSD shows fluctuations upto initial 25-30ns and then becomes very stable. I have performed PCA on the last 30ns window of the simulation where I assume the simulation has converged (I also did on other time windows as well). The question is this: I did the analysis on the last 30ns window in two ways by taking two different reference structures. a. I take the average structure of the trajectory (0-100ns) as the reference and then do the fitting and calculate covariance matrix for last 30ns. This is done because I suspect that the average structure over full trajectory will reflect all the changes occurring in the protein. It also gives me low cosines (0.1). The PCs show movement occurring in certain regions of the protein. b. I take the average structure from the same window (last 30ns) then do the fitting and calculate covariance matrix for the same. This is done with an assumption that the reference structure must reflect the equilibriated/stable part of the trajectory unlike the previous case. Surprisingly it gives me high cosines (0.5). Unlike the previous case, this method shows very small movement in the protein (very low RMSF). Both of these methods give me different RMSF for the PCs although they are done on the same part of the trajectory but the reference structure is influencing the output. Which protocol among the two is appropriate ? And how can we explain high cosines in second case where the reference structure is the average of the same time window (there must not be large deviation) while I get low cosine for the first case where deviations are calculated from the full trajectory average (large deviation) ? Any help is appreciated. Thanks, -Vivek Modi Graduate Student IITK. -- 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] Regarding manual velocity generation in simulation
Hello All, Please let me know whether is it possible to manually assign the velocity for each atom in the simulation instead of generating through gen_vel option. -- *--- 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] Essential dynamics (ED) sampling using make_edi
Hello All, I want to use the essential dynamics (ED) sampling method to simulate the unfolding to folding process using make_edi option of GROMACS. For this task I am using -radcon option (acceptance radius contraction along the first two eigenvectors towards the folded structure (b4md.gro)) of make_edi as below: *make_edi -f eigenvec.trr -eig eigenval.xvg -s topol.tpr -tar b4md.gro -radcon 1-2 -o sam.edi * *b4md.gro:* folded structure (C-alpha only) *topol.tpr: *all atom * eigenvec.trr*:from g_covar (C-alpha only) Is this is the correct way of doing the ED sampling... Also I am not sure about the following: *1)* How to judge the correct/appropriate value for the: -maxedsteps *2)* How to judge the appropriate values for the following parameters for an Essential dynamics sampling input *(or it is neglected for ED sampling and used only for flooding input ) * -deltaF0 -deltaF -tau -alpha -T *3) *Will the output trajectory (produced using mdrun -ei sam.edi ) contain all atoms or only the C-alpha atoms (using the above make_edi command). -- *--- 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] fraction of native contacts calculation
Thanks for your response. Hope to see this feature in upcoming GROMACS release. Before that, could it be possible to get the modified code in the user contribution section, it may be useful for many GROMACS users. On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund er...@xray.bmc.uu.se wrote: 31 okt 2012 kl. 13.43 skrev Justin Lemkul: On 10/31/12 6:02 AM, bipin singh wrote: Hello all, Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. At present, there is no way to do this. Likely one could modify the g_mindist code to do this - it would be a very nice feature. If one could get the -sel option of g_hbond to work again then you would get such information with -contact. Erik -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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 -- --- *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] fraction of native contacts calculation
Thanks for the information. On Thu, Nov 1, 2012 at 10:56 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/1/12 1:23 PM, bipin singh wrote: Thanks for your response. Hope to see this feature in upcoming GROMACS release. Before that, could it be possible to get the modified code in the user contribution section, it may be useful for many GROMACS users. If someone writes the code, certainly. Gromacs is a user-driven community, after all :) If there is a feature you want, file a feature request on redmine.gromacs.org, otherwise no one is likely to pay much attention to it, as other, much larger changes are ongoing. -Justin On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund er...@xray.bmc.uu.se wrote: 31 okt 2012 kl. 13.43 skrev Justin Lemkul: On 10/31/12 6:02 AM, bipin singh wrote: Hello all, Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. At present, there is no way to do this. Likely one could modify the g_mindist code to do this - it would be a very nice feature. If one could get the -sel option of g_hbond to work again then you would get such information with -contact. Erik -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists --**- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/**elflab/index.htmlhttp://www2.icm.uu.se/molbio/elflab/index.html -- 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. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- --- *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] fraction of native contacts calculation
Thanks a lot Oliver for the useful information. On Fri, Nov 2, 2012 at 12:26 AM, Oliver Beckstein obeck...@asu.edu wrote: Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. At present, there is no way to do this. Likely one could modify the g_mindist code to do this - it would be a very nice feature. If one could get the -sel option of g_hbond to work again then you would get such information with -contact. In the meantime you might be able to use MDAnalysis http://mdanalysis.googlecode.com/ and the native contact analysis in MDAnalysis.analysis.contacts, see http://packages.python.org/MDAnalysis/documentation_pages/analysis/contacts.html (If you have questions about MDAnalysis then please ask them on that project's discussion group http://groups.google.com/group/mdnalysis-discussion — people there are more than happy to help.) Best wishes, Oliver -- Oliver Beckstein * oliver.beckst...@asu.edu http://becksteinlab.physics.asu.edu/ Arizona State University Department of Physics Tempe, AZ 85287-1504 USA Office: PSF 348 Phone: +1 (480) 727-9765 FAX: +1 (480) 965-4669 Department of Physics: http://physics.asu.edu/home/people/faculty/oliver-beckstein Center for Biological Physics: http://biophysics.asu.edu/CBP/person.php?ID=343 -- 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 -- --- *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] fraction of native contacts calculation
Thanks a lot Sanku for your help. On Thu, Nov 1, 2012 at 11:38 PM, Sanku M msank...@yahoo.com wrote: Bipin, There might be a workaround. You might want to check out Plumed plugin in latest versions of VMD for calculating fractions of native contact. You can load the gromacs trajectory along with the native .gro file in VMD and use Plumed plugin inbuilt in VMD . You need to install plumed most probably early. From: bipin singh bipinel...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, November 1, 2012 1:23 PM Subject: Re: [gmx-users] fraction of native contacts calculation Thanks for your response. Hope to see this feature in upcoming GROMACS release. Before that, could it be possible to get the modified code in the user contribution section, it may be useful for many GROMACS users. On Thu, Nov 1, 2012 at 4:39 PM, Erik Marklund er...@xray.bmc.uu.se wrote: 31 okt 2012 kl. 13.43 skrev Justin Lemkul: On 10/31/12 6:02 AM, bipin singh wrote: Hello all, Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. At present, there is no way to do this. Likely one could modify the g_mindist code to do this - it would be a very nice feature. If one could get the -sel option of g_hbond to work again then you would get such information with -contact. Erik -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- 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 -- --- *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 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 -- --- *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] fraction of native contacts calculation
Hello all, Is there any way to calculate fraction of native contacts during the simulation in gromacs. I searched the archives but didn't found any significant clue. *-- --- 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] Angle between two six membered rings
Hello all, I was trying to calculate the normal-normal angle between the two six membered rings using g_sgangle. I was considering the 3 atoms to define the plane for each six membered ring but I am not getting the correct values of normal-normal angle from g_sgangle in this way. Please suggest me the correct way to calculate it in gromacs . -- --- 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] Segmentation fault while calculating water mediated H-bond with g_hbond
Hello all, I was trying to calculate solvent mediated H-bond between a amino acid residue (Tyr) and solvent molecule present within cutoff of 0.5nm (after creating separate index) with the help of g_hbond version 4.5.3. But I am getting segmentation fault while running g_hbond. Moreover I am getting error only for this particular residue, whereas with other residues the samilar calculation is working fine. I have used the following command for the calculation: g_hbond -f traj.xtc -s md.tpr -num hbnum.xvg -hbn hbond.ndx -g hbond.log -dist hbdist.xvg -hbm hbmap.xvg -n index.ndx Please provide your suggestions to rectify the error. -- --- *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] Regarding Pulling simulation:To study the base flipping of the thymine
Hi all, I am studying a system which consists of DNA duplex 20 base pairs. Actually I am interested in studying the base flipping of the thymine. I have the crystal structure of extrahelical DNA in which thymine is out side the helical structure. I want use pulling simulations to bring this base from extrahelical to Intrahelical conformation, is there any way to do it in GROMACS pull code. Please see the figure below (link) for description. http://researchweb.iiit.ac.in/~kartheek.p/extrintra.png -- Thanks and Regards, kartheek, -- 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] MD after equilibration phase
Also, if we give continuation=yes in mdp file and use input as pdb file as input instead of gro file, grompp never complainsI don't no how it reads velocities from pdb file (as no velocities are present in pdb files). Ideally it should complain that no velocities found in input file On Fri, Apr 6, 2012 at 12:42, Peter C. Lai p...@uab.edu wrote: On 2012-04-06 11:05:51AM +0400, James Starlight wrote: Dear Gromacs users! I have small question about order of the runs and input data. Ussually I do 2 equilibration phases and subsequent productive phase in the conditions wich are equal to the last equilibration phase ( e.g often this is npt ). In the second equil.mdp and md.mdp there is option continuation = yes which means that there have been previous phases of the simulation from wich coordinates and velocities should be taken. As I understood the coordinates is taken from .gro file but from what file the velocities must be providen ? Does it .cpt checkpoint file from previous run? In some cases I've forgotten to define -t npt.cpt for my MD run providing only coordinates in GRO file, topology and md.mdp but I have not seen any errors in such simulation due to absence of that .cpt and GROMPP never remind me of the absense of this file. What exactly is in that .cpt file and from wich source the velocities from equilibration phase are taken ? continuation = yes is telling LINCS that it is a continuation and it should not attempt to refit the constrained bonds on the first pass. The coords, velocities, state, and box information are taken either from the cpt file or you can specify the previous .trr and it will take the last frame from that and use it. If you used the output gro file without -t, then it will take coordinates and velocities from the .gro but the problem there is the limited precision (3 decimal points for each). -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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 -- --- *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] MD after equilibration phase
When we mention gen_vel=no ;And provide pdb as input with no velocities As mentioned in the manual: The velocities are set to zero when there are no velocities in the input structure file Please elaborate what does this sentence mean. On Fri, Apr 6, 2012 at 19:10, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Also, if we give continuation=yes in mdp file and use input as pdb file as input instead of gro file, grompp never complainsI don't no how it reads velocities from pdb file (as no velocities are present in pdb files). Ideally it should complain that no velocities found in input file Again, the continuation keyword has nothing to do with velocities. If you have gen_vel = no and you provide a .pdb file with no velocities, then you do not preserve velocity information. Whatever the initial forces are govern the resulting motions. In any case, you do not preserve the previous simulation conditions. -Justin On Fri, Apr 6, 2012 at 12:42, Peter C. Lai p...@uab.edu mailto: p...@uab.edu wrote: On 2012-04-06 11:05:51AM +0400, James Starlight wrote: Dear Gromacs users! I have small question about order of the runs and input data. Ussually I do 2 equilibration phases and subsequent productive phase in the conditions wich are equal to the last equilibration phase ( e.g often this is npt ). In the second equil.mdp and md.mdp there is option continuation = yes which means that there have been previous phases of the simulation from wich coordinates and velocities should be taken. As I understood the coordinates is taken from .gro file but from what file the velocities must be providen ? Does it .cpt checkpoint file from previous run? In some cases I've forgotten to define -t npt.cpt for my MD run providing only coordinates in GRO file, topology and md.mdp but I have not seen any errors in such simulation due to absence of that .cpt and GROMPP never remind me of the absense of this file. What exactly is in that .cpt file and from wich source the velocities from equilibration phase are taken ? continuation = yes is telling LINCS that it is a continuation and it should not attempt to refit the constrained bonds on the first pass. The coords, velocities, state, and box information are taken either from the cpt file or you can specify the previous .trr and it will take the last frame from that and use it. If you used the output gro file without -t, then it will take coordinates and velocities from the .gro but the problem there is the limited precision (3 decimal points for each). -- ==**==**== Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu mailto:p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ==**==**== -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- --- /Regards,/ Bipin Singh -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- --- *Regards,* Bipin Singh
Re: [gmx-users] MD after equilibration phase
Thanks for your comments. One more question. Does Gromacs saves velocities in pdb files, when we use gen_vel=yes option in mdp and save the output(-c) of mdrun as pdb file instead of gro file. On Fri, Apr 6, 2012 at 19:48, Mark Abraham mark.abra...@anu.edu.au wrote: On 7/04/2012 12:15 AM, bipin singh wrote: When we mention gen_vel=no ;And provide pdb as input with no velocities As mentioned in the manual: The velocities are set to zero when there are no velocities in the input structure file Please elaborate what does this sentence mean. Each atom must have a velocity in a *dynamical* simulation. If there is no instruction for what values to use (i.e. not generated or supplied), zero is used. Integration proceeds from there, and this may or may not be stable, and certainly will not have the desired temperature (yet)... Mark On Fri, Apr 6, 2012 at 19:10, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Also, if we give continuation=yes in mdp file and use input as pdb file as input instead of gro file, grompp never complainsI don't no how it reads velocities from pdb file (as no velocities are present in pdb files). Ideally it should complain that no velocities found in input file Again, the continuation keyword has nothing to do with velocities. If you have gen_vel = no and you provide a .pdb file with no velocities, then you do not preserve velocity information. Whatever the initial forces are govern the resulting motions. In any case, you do not preserve the previous simulation conditions. -Justin On Fri, Apr 6, 2012 at 12:42, Peter C. Lai p...@uab.edu mailto: p...@uab.edu wrote: On 2012-04-06 11:05:51AM +0400, James Starlight wrote: Dear Gromacs users! I have small question about order of the runs and input data. Ussually I do 2 equilibration phases and subsequent productive phase in the conditions wich are equal to the last equilibration phase ( e.g often this is npt ). In the second equil.mdp and md.mdp there is option continuation = yes which means that there have been previous phases of the simulation from wich coordinates and velocities should be taken. As I understood the coordinates is taken from .gro file but from what file the velocities must be providen ? Does it .cpt checkpoint file from previous run? In some cases I've forgotten to define -t npt.cpt for my MD run providing only coordinates in GRO file, topology and md.mdp but I have not seen any errors in such simulation due to absence of that .cpt and GROMPP never remind me of the absense of this file. What exactly is in that .cpt file and from wich source the velocities from equilibration phase are taken ? continuation = yes is telling LINCS that it is a continuation and it should not attempt to refit the constrained bonds on the first pass. The coords, velocities, state, and box information are taken either from the cpt file or you can specify the previous .trr and it will take the last frame from that and use it. If you used the output gro file without -t, then it will take coordinates and velocities from the .gro but the problem there is the limited precision (3 decimal points for each). -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu mailto:p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- --- /Regards,/ Bipin Singh -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un
Re: [gmx-users] MD after equilibration phase
Thanks for your comments I have a very crude question which may not be even logical to ask here but I just want to know your opinion on this: If I will perform two simulations in following two ways : *RUN:1* (1) Did NVT with POSRES on protein and gen_vel=yes gen_temp= 350 (2) Did NPT with POSRES on protein and continuation=yes gen_vel=no ;Without reading velocities from NVT (3) Did MD with No POSRES (NPT) continuation=yes gen_vel=no ; No velocities read from previous run * RUN:2 *(1) Did NVT with POSRES on protein and gen_vel=yes gen_temp= 350 (2) Did NPT with POSRES on protein and continuation=yes gen_vel=no ; Reading velocities from NVT run using -t option (3) Did MD with No POSRES (NPT) continuation=yes gen_vel=no ; Velocities read from previous run using -t option What will be the expected flaws of the RUN:1 over RUN:2 and will the results got from the RUN:1 is unreliable ? If yes why ? On Fri, Apr 6, 2012 at 20:26, Mark Abraham mark.abra...@anu.edu.au wrote: On 7/04/2012 12:37 AM, Justin A. Lemkul wrote: bipin singh wrote: Thanks for your comments. One more question. Does Gromacs saves velocities in pdb files, when we use gen_vel=yes option in mdp and save the output(-c) of mdrun as pdb file instead of gro file. No. Velocities are only saved in the .trr and/or .cpt files. There is no place for velocities in .pdb files. It's conceivable that there are velocities in a mdrun -c finalstructure.gro file, but these would have to be only at low precision, and thus often useless. Mark -- 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 -- --- *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] Different results from identical tpr after MD
Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. -- --- *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] Different results from identical tpr after MD
Thanks for the reply. * *I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. And also how to believe the statement made by several research papers based on unconverged simulations. On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. It is not unexpected at all. Please consult: http://www.gromacs.org/**Documentation/Terminology/**Reproducibilityhttp://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- --- *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] Different results from identical tpr after MD
Yes you are right, that we need to do multiple MD runs before making any conclusion based on single trajectory. But I have not found any single research paper which discuss about conclusions drawn based on ensemble of trajectories. If you have any such research article then please send me the link. On Thu, Apr 5, 2012 at 23:50, Peter C. Lai p...@uab.edu wrote: Well you're really supposed to conduct multiple runs anyway. Remember, a single MD run over a period of time only samples 1 possible trajectory out of the ensemble of possible trajectories... On 2012-04-05 11:38:20PM +0530, bipin singh wrote: Thanks for the reply. * *I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. And also how to believe the statement made by several research papers based on unconverged simulations. On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. It is not unexpected at all. Please consult: http://www.gromacs.org/**Documentation/Terminology/**Reproducibility http://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- 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 -- --- *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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | == -- 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
Re: [gmx-users] Different results from identical tpr after MD
Thanks for your valuable suggestions. I am totally agree with your views. On Fri, Apr 6, 2012 at 00:11, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for the reply. / /I read the link. So, how one can predict something reliable using these results(based on 50ns in my case) which changes on different machines? which depends more on the environment of the computer architecture and other variables of mdrun rather than system (Protein/DNA/RNA) itself for a short simulation, where we don't have enough resources to run infinitely long simulation. No one can do anything for an infinite amount of time ;) Hence replicate simulations and thorough statistical analysis are required to obtain reliable results and prove that what you've done is to be trusted. The other comments in this thread are quite good so I won't recapitulate other points that have been made. And also how to believe the statement made by several research papers based on unconverged simulations. I wouldn't trust any conclusions drawn from demonstrably unconverged simulations. Not everything that's published has been done correctly. Peer review is an imperfect system, so be careful what you read and apply good scientific judgment. -Justin On Thu, Apr 5, 2012 at 23:12, Justin A. Lemkul jalem...@vt.edu mailto: jalem...@vt.edu wrote: bipin singh wrote: Hi all, I am really surprised to see different results from two identical md simulation. I have used identical tpr files for the mdrun (for 50ns) and after the completion of the md job I found that the results from the identical runs is totally different. To further confirm this, I have converted both the input tpr to mdp using gmxdump and diff the two files and found that the mdp is identical. Please let me know what can be the reason of this behaviour. I know that it is unexpected and even I can't believe how can it be possible. It is not unexpected at all. Please consult: http://www.gromacs.org/__**Documentation/Terminology/__** Reproducibilityhttp://www.gromacs.org/__Documentation/Terminology/__Reproducibility http://www.gromacs.org/**Documentation/Terminology/**Reproducibilityhttp://www.gromacs.org/Documentation/Terminology/Reproducibility -Justin -- ==**__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users 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/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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 mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- --- /Regards,/ Bipin Singh -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- --- *Regards,* Bipin Singh
[gmx-users] Pressure coupling doubt
Hello, I have two doubts regarding pressure coupling in Gromacs: 1) When I use pcoupl=no the mdp.out shows the following ; Pressure coupling pcoupl = no Pcoupltype = Isotropic nstpcouple = -1 ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p= 1 compressibility = ref-p= I have not used the pcoupl(=no) then why it is showing Pcoupltype=Isotropic. (2) This is a silly question: What will happen if we use following option in mdp of NVT simulation: pcoupl=no compressibility= 4.5e-5 does it will affect the NVT criteria ? or It will ignore the compressibility input? -- --- 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] Pressure coupling and Isothermal compressibility for a biphasic system
Hello All, I have some doubts regarding the use of pressure coupling and isothermal compressibility for a biphasic system (octane+water boxes built over each other). I have two questions regarding that: (1) Which pressure coupling (pcoupl) type would be suitable for this type of system ? (2) As water and octane have different compressibility, is it possible to mention the compressibility of water and octane separately? Please provide your suggestions. -- --- 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] Re: How to add dihedral information from the GAFF topology
Thanks for your inputs. I have checked the coordinate file thoroughly and the order of atoms are same as defined in the [molecules] directive. I really do not able to find out the source of the error. On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul jalem...@vt.edu wrote: Biswajit Gorai wrote: Dear Bipin, Edit your topology file as: ### ; Include forcefield parameters #include amber99sb-ildn.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Ion_chain_A2.itp *#include oct.itp* If oct.itp introduces new atom types (as the original .top does, for GAFF), placing this topology here will result in a fatal error since there is a new [atomtypes] directive that is introduced after the protein [moleculetype]. If oct.itp does not introduce any new atom types, its location within the system topology is irrelevant. ; Include water topology #include amber99sb-ildn.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include amber99sb-ildn.ff/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein_chain_A 1 Ion_chain_A2 1 *1-octanol 1 * *SOL 8987* Depending on the order of the coordinate file, it may not be possible to merge the SOL entries in this way. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- --- 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] Re: How to add dihedral information from the GAFF topology
A lot of thanks to your charitable mood now the things has been resolved :) . Thanks again. On Wed, Mar 28, 2012 at 18:24, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks again For the record, I didn't ask that you send me your files so I could troubleshoot for you. Luckily for you I'm in a charitable mood this morning, so I took a look ;) Your problem is that you have a [molecules] directive in oct.itp. Please refer to the documentation for the difference between a .top topology and a .itp topology: http://www.gromacs.org/Documentation/File_Formats/.itp_File The presence of this [molecules] directive tells grompp that the first thing it should expect is a block of octanol, when in fact your coordinate file has the protein first (starting with Ser-Leu, as I suspected). You then have 1-octanol 1 in your topol.top, which says you're including another random octanol molecule somewhere later. You need a single [molecules] directive in the .top, which must match the order of the coordinate file. Once you've got that, things should work fine. -Justin From the error It seems that I have placed the octane molecule before the protein but it is not the case, I dont know why grompp is reading parameters for octane first and expecting it to match with protein. I know that its my problem and I have to think about that but just for the reference for you I am attaching the coordinate and topology files. On Wed, Mar 28, 2012 at 16:19, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your inputs. I have checked the coordinate file thoroughly and the order of atoms are same as defined in the [molecules] directive. I really do not able to find out the source of the error. Looking closer at the error, what's happening is your octanol molecule is in a place where the topology expects the amino acid sequence Ser-Leu. Perhaps that will help you track down the source of the problem. It seems to me that your octanol molecule occurs earlier in the coordinate file than it does in the topology. If you still can't locate the problem, then you can always start over building your system in a known order, checking the alignment of the coordinate file and topology at every step. -Justin On Wed, Mar 28, 2012 at 08:55, Justin A. Lemkul jalem...@vt.edu wrote: Biswajit Gorai wrote: Dear Bipin, Edit your topology file as: ### ; Include forcefield parameters #include amber99sb-ildn.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Ion_chain_A2.itp *#include oct.itp* If oct.itp introduces new atom types (as the original .top does, for GAFF), placing this topology here will result in a fatal error since there is a new [atomtypes] directive that is introduced after the protein [moleculetype]. If oct.itp does not introduce any new atom types, its location within the system topology is irrelevant. ; Include water topology #include amber99sb-ildn.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include amber99sb-ildn.ff/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein_chain_A 1 Ion_chain_A2 1 *1-octanol 1 * *SOL 8987* Depending on the order of the coordinate file, it may not be possible to merge the SOL entries in this way. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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
Re: [gmx-users] Re: How to add dihedral information from the GAFF topology
Thanks for your inputs. I have followed your suggestion and included the .itp for the octane molecule (containing atomtype definition for new atoms) in the topology file(.top) of the whole system (prot+oct+water). but during grompp it produce error and results in termination due to non matching numbers (27 atoms of octane molecule) between coordinate file and topology file. WARNING 1 [file 111-87-5.top, line 15]: Overriding atomtype h1 WARNING 2 [file 111-87-5.top, line 17]: Overriding atomtype c3 WARNING 3 [file 111-87-5.top, line 19]: Overriding atomtype ho Generated 4656 of the 4656 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 4656 of the 4656 1-4 parameter combinations Excluding 3 bonded neighbours molecule type '1-octanol' Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 3 bonded neighbours molecule type 'Ion_chain_A2' Excluding 3 bonded neighbours molecule type '1-octanol' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 55]: System has non-zero total charge: -9.89e-01 Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (box_oct_sol.gro, 54297) does not match topology (topol.top, 54324) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ##3 this is how I included the itp for the octane molecule in .top file ; Include forcefield parameters #include amber99sb-ildn.ff/forcefield.itp #include octane.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Ion_chain_A2.itp ; Include water topology #include amber99sb-ildn.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include amber99sb-ildn.ff/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Ion_chain_A21 1-octanol 1 SOL 565 SOL 8495 # --- Please provide your comments. On Tue, Mar 27, 2012 at 03:20, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your reply. Yes, you are right that these topologies are self supporting and there is no need to to call any other information. I followed your suggestions and able to generate a biphasic system of water/octane containing a protein molecule. But, when I tried grompp on this biphasic system (containing octane+water+protein), it results in error even if I include the topologies in forcefield.itp file. The error was Fatal error: Atomtype hc not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors If you introduce a new atomtype in your topology somewhere (presumably in one of the GAFF topologies), then you have to declare them in an [atomtypes] directive in the appropriate place in the .top file. These types are case sensitive as well. For dealing with GAFF-type topologies, assuming you can #include them within whatever AMBER force field you've chosen (up to you to prove), you can do something like: #include amberXX.ff/forcefield.itp #include ligand.itp [ moleculetype ] ;name nrexcl Protein 3 (etc) The inclusion of the ligand topology (at this specific location) will add the new [atomtypes] at the appropriate level of precedence, before any [moleculetypes] are declared. -Justin On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your reply. But as far as I understood, in order to use these GAFF topology (for e.g. to perform simulation using these topologies) with Gromacs we have to incorporate the information from these topologies to the existing Amber forcefields in Gromacs or Is there anyway (Possibility of using Standalone GAFF parameters in Gromacs) to do it without performing this task. As David said, the topologies stand on their own. You do not need to call any further information from anywhere. The .top that you downloaded begins with a [defaults] directive, declares atom types, and proceeds through the rest of the topology with explicit parameters. As you said these topologies are self supporting and we do not need to change ffbonded.itp, but during grompp I got the following error, may be because I have not added the dihedral information. ERROR [file oct.top]: No default Proper Dih. types Please provide your suggestions. I certainly don't see how
Re: [gmx-users] Re: How to add dihedral information from the GAFF topology
Thanks for your suggestions. Now I am getting the following error during grompp Warning: atom name 1 in topol.top and box_prot_oct_sol.gro does not match (C1 - N) Warning: atom name 5 in topol.top and box_prot_oct_sol.gro does not match (C2 - CA) Warning: atom name 6 in topol.top and box_prot_oct_sol.gro does not match (H4 - HA) Warning: atom name 7 in topol.top and box_prot_oct_sol.gro does not match (H5 - CB) Warning: atom name 8 in topol.top and box_prot_oct_sol.gro does not match (C3 - HB1) Warning: atom name 9 in topol.top and box_prot_oct_sol.gro does not match (H6 - HB2) Warning: atom name 10 in topol.top and box_prot_oct_sol.gro does not match (H7 - OG) Warning: atom name 11 in topol.top and box_prot_oct_sol.gro does not match (C4 - HG) Warning: atom name 12 in topol.top and box_prot_oct_sol.gro does not match (H8 - C) Warning: atom name 13 in topol.top and box_prot_oct_sol.gro does not match (H9 - O) Warning: atom name 14 in topol.top and box_prot_oct_sol.gro does not match (C5 - N) Warning: atom name 15 in topol.top and box_prot_oct_sol.gro does not match (H10 - H) Warning: atom name 16 in topol.top and box_prot_oct_sol.gro does not match (H11 - CA) Warning: atom name 17 in topol.top and box_prot_oct_sol.gro does not match (C6 - HA) Warning: atom name 18 in topol.top and box_prot_oct_sol.gro does not match (H12 - CB) Warning: atom name 19 in topol.top and box_prot_oct_sol.gro does not match (H13 - HB1) Warning: atom name 20 in topol.top and box_prot_oct_sol.gro does not match (C7 - HB2) Warning: atom name 21 in topol.top and box_prot_oct_sol.gro does not match (H14 - CG) Warning: atom name 22 in topol.top and box_prot_oct_sol.gro does not match (H15 - HG) Warning: atom name 23 in topol.top and box_prot_oct_sol.gro does not match (C8 - CD1) (more than 20 non-matching atom names) WARNING 1 [file topol.top, line 55]: 28782 non-matching atom names atom names from topol.top will be used atom names from box_prot_oct_sol.gro will be ignored The order of atoms in coordinate file and order of [molecules] directive are same. I have checked on the gromacs forum and also the documentation but not able to rectify the problem. This is how I included the octane topology in .top file # ; Include forcefield parameters #include amber99sb-ildn.ff/forcefield.itp #include oct.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Ion_chain_A2.itp ; Include water topology #include amber99sb-ildn.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include amber99sb-ildn.ff/ions.itp [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Ion_chain_A21 SOL 565 1-octanol 1 SOL 8422 Please provide suggestions. On Tue, Mar 27, 2012 at 17:59, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your inputs. I have followed your suggestion and included the .itp for the octane molecule (containing atomtype definition for new atoms) in the topology file(.top) of the whole system (prot+oct+water). but during grompp it produce error and results in termination due to non matching numbers (27 atoms of octane molecule) between coordinate file and topology file. WARNING 1 [file 111-87-5.top, line 15]: Overriding atomtype h1 WARNING 2 [file 111-87-5.top, line 17]: Overriding atomtype c3 WARNING 3 [file 111-87-5.top, line 19]: Overriding atomtype ho It appears that you have somehow duplicated atom types and they are overriding each other. Generated 4656 of the 4656 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 4656 of the 4656 1-4 parameter combinations Excluding 3 bonded neighbours molecule type '1-octanol' Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 3 bonded neighbours molecule type 'Ion_chain_A2' Excluding 3 bonded neighbours molecule type '1-octanol' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 55]: System has non-zero total charge: -9.89e-01 Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (box_oct_sol.gro, 54297) does not match topology (topol.top, 54324) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Did you follow the link? Surely you would have found: http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology -Justin ##3 this is how I
[gmx-users] How to add dihedral information from the GAFF topology
Hello all, I am using the GAFF topology provided for octan-1-ol at Gromacs liquid database (http://virtualchemistry.org/molecules/111-87-5/index.php). I have incorporated all the parameters for atoms, bonds and non-bonded interaction type in the forcefield (Amber99sb-ildn in Gromacs) from GAFF topology (111-87-5.top), but I am not sure how to add the dihedraltypes information in ffbonded.itp from the GAFF topology as to add this information I need the phase and kd for each dihedral. Is this information is available in the GAFF topology provided in the Gromacs database ? -- --- 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] Re: How to add dihedral information from the GAFF topology
Thanks for your reply. But as far as I understood, in order to use these GAFF topology (for e.g. to perform simulation using these topologies) with Gromacs we have to incorporate the information from these topologies to the existing Amber forcefields in Gromacs or Is there anyway (Possibility of using Standalone GAFF parameters in Gromacs) to do it without performing this task. As you said these topologies are self supporting and we do not need to change ffbonded.itp, but during grompp I got the following error, may be because I have not added the dihedral information. ERROR [file oct.top]: No default Proper Dih. types Please provide your suggestions. On Mon, Mar 26, 2012 at 17:29, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2012-03-26 13:55, bipin singh wrote: Hello all, I am using the GAFF topology provided for octan-1-ol at Gromacs liquid database (http://virtualchemistry.org/molecules/111-87-5/index.php). I have incorporated all the parameters for atoms, bonds and non-bonded interaction type in the forcefield (Amber99sb-ildn in Gromacs) from GAFF topology (111-87-5.top), but I am not sure how to add the dihedraltypes information in ffbonded.itp from the GAFF topology as to add this information I need the phase and kd for each dihedral. Is this information is available in the GAFF topology provided in the Gromacs database ? This topology is self supporting and you do not need anything else in ffbonded.itp. You should be careful merging such parameters with an existing force field, because strictly speaking these are different force fields. -- 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.se http://folding.bmc.uu.se -- 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 -- --- 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] Re: How to add dihedral information from the GAFF topology
Thanks for your reply. Yes, you are right that these topologies are self supporting and there is no need to to call any other information. I followed your suggestions and able to generate a biphasic system of water/octane containing a protein molecule. But, when I tried grompp on this biphasic system (containing octane+water+protein), it results in error even if I include the topologies in forcefield.itp file. The error was Fatal error: Atomtype hc not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your reply. But as far as I understood, in order to use these GAFF topology (for e.g. to perform simulation using these topologies) with Gromacs we have to incorporate the information from these topologies to the existing Amber forcefields in Gromacs or Is there anyway (Possibility of using Standalone GAFF parameters in Gromacs) to do it without performing this task. As David said, the topologies stand on their own. You do not need to call any further information from anywhere. The .top that you downloaded begins with a [defaults] directive, declares atom types, and proceeds through the rest of the topology with explicit parameters. As you said these topologies are self supporting and we do not need to change ffbonded.itp, but during grompp I got the following error, may be because I have not added the dihedral information. ERROR [file oct.top]: No default Proper Dih. types Please provide your suggestions. I certainly don't see how this could have happened. All the dihedral parameters are listed explicitly. The fatal error should have printed a line number in the .top that is problematic, so start by investigating there. If you have modified the topology in any way, then undo the changes and try again. I did not have any trouble using this .top in an unmodified form, so I suspect you've altered it in some way that has broken it. -Justin On Mon, Mar 26, 2012 at 17:29, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2012-03-26 13:55, bipin singh wrote: Hello all, I am using the GAFF topology provided for octan-1-ol at Gromacs liquid database (http://virtualchemistry.org/molecules/111-87-5/index.php). I have incorporated all the parameters for atoms, bonds and non-bonded interaction type in the forcefield (Amber99sb-ildn in Gromacs) from GAFF topology (111-87-5.top), but I am not sure how to add the dihedraltypes information in ffbonded.itp from the GAFF topology as to add this information I need the phase and kd for each dihedral. Is this information is available in the GAFF topology provided in the Gromacs database ? This topology is self supporting and you do not need anything else in ffbonded.itp. You should be careful merging such parameters with an existing force field, because strictly speaking these are different force fields. -- 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.se http://folding.bmc.uu.se -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- --- 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] Simulated Annealing Protocol...
continuation =yes so my Queries are 1. As I not define = -DPOSRES in SA mdp is it sound well???, should I have to run Production run after my SA run(That means Is SA is substitute to Production run ??) ??? or I have to use define = -DPOSRES in my SA mdp , and then I have to do production run 2. Or as per Justin recommendation NVT at 277 ,followed by SA (Then I have to use define = -DPOSRES in My SA mdp file ,Is it right??) then NPT afterward Production run .. So what is your suggestion ??? The answers to your question depend entirely upon what you want to do and observe. If you're using SA simply as part of an equilibration protocol (as I often do, which was what I based my suggestion upon earlier), then I stick with my protocol, which is point #2. If you're trying to model the behavior of your system in response to a change in termperature, then SA is your production run and you would not use position restraints. It is still not clear to me how you wish to use SA or what you hope to observe from it, so that's the best I can offer. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- --- 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] Regarding DispCorr
Hello, Please let me know, Whether it is correct to use DispCorr=EnerPres during energy minimization. -- --- 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] Regarding DispCorr
Hello, Thanks for reply. As given in the manual, If we give DispCorr=EnerPres it will apply long range dispersion corrections for Energy and Pressure. But I don't know whether it is logical to apply this during energy minimization. On Sun, Feb 19, 2012 at 20:20, Mark Abraham mark.abra...@anu.edu.au wrote: On 19/02/2012 11:21 PM, bipin singh wrote: Hello, Please let me know, Whether it is correct to use DispCorr=EnerPres during energy minimization. What does it do? Mark -- 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 -- --- 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] Regarding DispCorr
Thank you so much Sir for clearing my doubts. I understood your point. On Mon, Feb 20, 2012 at 12:51, Mark Abraham mark.abra...@anu.edu.au wrote: On 20/02/2012 4:19 PM, bipin singh wrote: Thanks for your help. But I am getting different results for potential energy when minimization done applying DispCorr=EnerPres and minimization done without DispCorr. Please provide your suggestions They will be different, but they are highly unlikely to be *significantly* different. Slight changes in the nearly symmetric effect of long-range interactions are not going to change the general nature of the local minimum that you approach with EM - and decidedly not if all you are doing is preparing to do dynamics. Doing those dynamics is a different matter. Mark My mdp for minimization is as follows: define= -DFLEXIBLE constraints = none integrator= steep dt= 0.002; ps ! nsteps= 50 nstlist= 1 ns_type= grid rlist= 1.0 coulombtype= PME vdwtype= cut-off rcoulomb= 1.0 rvdw= 1.0 DispCorr=EnerPres ; (and No DispCorr for other case) fourierspacing= 0.12 fourier_nx= 0 fourier_ny= 0 fourier_nz= 0 pme_order= 4 ewald_rtol= 1e-5 optimize_fft= yes emtol=100.0 emstep=0.01 pbc=xyz On Mon, Feb 20, 2012 at 05:03, Mark Abrahammark.abra...@anu.edu.**aumark.abra...@anu.edu.au wrote: On 20/02/2012 2:23 AM, bipin singh wrote: Hello, Thanks for reply. As given in the manual, If we give DispCorr=EnerPres it will apply long range dispersion corrections for Energy and Pressure. But I don't know whether it is logical to apply this during energy minimization. Manual 4.8 sets out some conditions for its use. It is likely from the nature of EM that it doesn't matter either way. Mark On Sun, Feb 19, 2012 at 20:20, Mark Abrahammark.abra...@anu.edu.**aumark.abra...@anu.edu.au wrote: On 19/02/2012 11:21 PM, bipin singh wrote: Hello, Please let me know, Whether it is correct to use DispCorr=EnerPres during energy minimization. What does it do? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-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 -- --- *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] Regarding free energy calculation
Thanks a lot for your suggestions. On Mon, Dec 19, 2011 at 21:00, David Mobley dmob...@gmail.com wrote: Yes, changing the net charge of the system is something that is rather complicated in fact (one can plunge ahead and do it while ignoring the complications, but the results will typically be rather system-size dependent and essentially wrong). For more details refer to the Kastenholz and Hunenberger papers from J. Chem. Phys (2006 or 2007) and references therein. The good news is that for simple spherical ions KH have worked out the relevant corrections. The bad news is that if you move away from simple spherical ions you've got problems. David Mobley On Fri, Dec 16, 2011 at 6:41 AM, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I am willing to study the free energy of binding of a cation (Ca++) to the protein and I am following the free energy tutorial provided by Justin (http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** gmx-tutorials/free_energyhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy ). Please let me know whether the settings for this type of study would be same as given in the tutorial for ligand-Protein binding free energy calculation or it need some different approach: By decoupling a Ca2+ ion, you are removing 2 charges from the system. I don't know how to properly treat such a case (perhaps someone else can comment), but likely you'll find such topics in the literature. A better approach may be umbrella sampling, but again the literature should point you to reasonable methodology. I'm sure others have dealt with such questions before. -Justin The setting from the ligand-Protein binding free energy calculation are given as: van der Waals coupling: sc-alpha = 0.5 ; use soft-core for LJ (de)coupling sc-sigma = 0.3 sc-power = 1 couple-moltype= LIG couple-intramol = no couple-lambda0= none; non-interacting dummy in state A couple-lambda1= vdw ; only vdW terms on in state B Coulombic coupling: sc-alpha = 0 ; soft-core during (dis)charging can be unstable! sc-sigma = 0 couple-moltype= LIG couple-intramol = no couple-lambda0= vdw ; only vdW terms in state A (the previous state B is now A) couple-lambda1= vdw-q ; all nonbonded interactions are on in state B -- ==**== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- David Mobley dmob...@gmail.com 504-383-3662 -- 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 -- --- *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] Regarding free energy calculation
Hello, I am willing to study the free energy of binding of a cation (Ca++) to the protein and I am following the free energy tutorial provided by Justin (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy ). Please let me know whether the settings for this type of study would be same as given in the tutorial for ligand-Protein binding free energy calculation or it need some different approach: The setting from the ligand-Protein binding free energy calculation are given as: van der Waals coupling: sc-alpha = 0.5 ; use soft-core for LJ (de)coupling sc-sigma = 0.3 sc-power = 1 couple-moltype= LIG couple-intramol = no couple-lambda0= none; non-interacting dummy in state A couple-lambda1= vdw ; only vdW terms on in state B Coulombic coupling: sc-alpha = 0 ; soft-core during (dis)charging can be unstable! sc-sigma = 0 couple-moltype= LIG couple-intramol = no couple-lambda0= vdw ; only vdW terms in state A (the previous state B is now A) couple-lambda1= vdw-q ; all nonbonded interactions are on in state B -- --- 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] Unit of r in radial distribution function
Hello, Please let me know what is the unit of r (nm or A) in the radial distribution function output(rdf.xvg) of the program g_rdf in gromacs. As the output shows no units. -- --- 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] Unit of r in radial distribution function
Thanks. On Wed, Nov 30, 2011 at 20:06, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin, Gromacs uses nm. Cheers, Tsjerk On Wed, Nov 30, 2011 at 3:32 PM, bipin singh bipinel...@gmail.com wrote: Hello, Please let me know what is the unit of r (nm or A) in the radial distribution function output(rdf.xvg) of the program g_rdf in gromacs. As the output shows no units. -- --- Regards, Bipin Singh -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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 -- --- 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] Regarding inter helical distance using g_bundle
Hello, I want to calculate inter helical distance between two helices using g_bundle. As mentioned in the manual that g_bundle reads two index groups and divides both of them in -na parts. The centers of mass of these parts define the tops and bottoms of the axes. Please suggest me out of two possible options given below which one is the correct way of defining two index groups for calculating inter helical distance : (1) Atom1(CA) and Atom3(CA) in one index and Atom2 and Atom4 in another index (2) Atom1(CA) and Atom2(CA) in one index and Atom3 and Atom4 in another index For reference I am sending the link of figure with above Atom labels. http://researchweb.iiit.ac.in/~bipin.singh/helix.html Please have a look at the figure and provide your suggestions. --- 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] Regarding inter helical distance using g_bundle
Thanks for the suggestion. I will try that. On Tue, Nov 29, 2011 at 19:33, Gianluca Santoni gianluca.sant...@ibs.fr wrote: On 11/29/11 2:10 PM, bipin singh wrote: Hello, I want to calculate inter helical distance between two helices using g_bundle. As mentioned in the manual that g_bundle reads two index groups and divides both of them in -na parts. The centers of mass of these parts define the tops and bottoms of the axes. Please suggest me out of two possible options given below which one is the correct way of defining two index groups for calculating inter helical distance : (1) Atom1(CA) and Atom3(CA) in one index and Atom2 and Atom4 in another index (2) Atom1(CA) and Atom2(CA) in one index and Atom3 and Atom4 in another index For reference I am sending the link of figure with above Atom labels. http://researchweb.iiit.ac.in/~bipin.singh/helix.html Please have a look at the figure and provide your suggestions. --- Regards, Bipin Singh I think g_dist is a easier choice. -- Gianluca Santoni, Institut de Biologie Structurale 41 rue Horowitz Grenoble _ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -- 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 -- --- 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] Regarding cosine content
Hello all, I have done PCA from 50ns long trajectory for two similar proteins (length 180 aa and RMSD 0.2 A). The equilibration time and final simulation condition were identical for both the protein. But when I checked the cosine content for PC1 for both proteins they were 0.9 and 0.5 respectively. What can be the reason for this huge difference in cosine content of the two proteins ? -- --- 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] Regarding cosine content
Thanks for the reply... I calculated principal components per protein using the command g_anaeig -f md.xtc -s md.tpr -v eigenvec.trr -eig eigenval.xvg -comp eigcomp.xvg -rmsf eigrmsf.xvg -2d 2dproj.xvg -proj proj.xvg -tu ns -extr extr.pdb -filt filt.xtc -first 1 -last 2 Also please suggest how one can differentiate between the two scenarios, when the high cosine content is due to random diffusion or conformational changes ? On Thu, Nov 17, 2011 at 17:34, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin, It seems one of the proteins is taking longer to reach an equilibrium. Maybe it is undergoing a conformational change? Did you calculate the principal components per protein, or for the joint trajectories? It would have been better to echo the commands you used on the list, because it might result in a different interpretation. I also made some comments on the list a short while ago regarding the interpretation of projections and cosine content. Maybe they can help you form a picture of what is happening :) Hope it helps, Tsjerk On Thu, Nov 17, 2011 at 12:22 PM, bipin singh bipinel...@gmail.com wrote: Hello all, I have done PCA from 50ns long trajectory for two similar proteins (length 180 aa and RMSD 0.2 A). The equilibration time and final simulation condition were identical for both the protein. But when I checked the cosine content for PC1 for both proteins they were 0.9 and 0.5 respectively. What can be the reason for this huge difference in cosine content of the two proteins ? -- --- Regards, Bipin Singh -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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 -- --- 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] Regarding cosine content
Thanks for the reply... I calculated principal components per protein using the command g_anaeig -f md.xtc -s md.tpr -v eigenvec.trr -eig eigenval.xvg -comp eigcomp.xvg -rmsf eigrmsf.xvg -2d 2dproj.xvg -proj proj.xvg -tu ns -extr extr.pdb -filt filt.xtc -first 1 -last 2 Also please suggest how one can differentiate between the two scenarios, when the high cosine content is due to random diffusion or conformational changes ? On Thu, Nov 17, 2011 at 17:34, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin, It seems one of the proteins is taking longer to reach an equilibrium. Maybe it is undergoing a conformational change? Did you calculate the principal components per protein, or for the joint trajectories? It would have been better to echo the commands you used on the list, because it might result in a different interpretation. I also made some comments on the list a short while ago regarding the interpretation of projections and cosine content. Maybe they can help you form a picture of what is happening :) Hope it helps, Tsjerk On Thu, Nov 17, 2011 at 12:22 PM, bipin singh bipinel...@gmail.com wrote: Hello all, I have done PCA from 50ns long trajectory for two similar proteins (length 180 aa and RMSD 0.2 A). The equilibration time and final simulation condition were identical for both the protein. But when I checked the cosine content for PC1 for both proteins they were 0.9 and 0.5 respectively. What can be the reason for this huge difference in cosine content of the two proteins ? -- --- Regards, Bipin Singh -- 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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 -- --- Regards, Bipin Singh -- --- 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] Implicit solvation
Check the below link: http://www.gromacs.org/Documentation/Terminology/Implicit_Solvent On Mon, Oct 17, 2011 at 13:47, Soumya Lipsa Rath soumyalips...@gmail.com wrote: I am a new gromacs user. I wanted to simulate a membrane protein without the lipid bilayer using the IMM1 force field of CHARMM27. I really would appreciate if someone can help me solve this or direct me towards implicit solvation tutorial in gromacs Regards, Soumya -- 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 -- --- 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] CHARMM GUI to Gromacs
There is already tutorial for creating lipid bilayer and insertion of protein into that for GROMACS http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html Why you have used Charmmgui I am not able to understand. You can get some useful topologies from below link,but I don't know how useful it might be for your case. http://people.ucalgary.ca/~tieleman/download.html On Mon, Oct 17, 2011 at 14:31, Roy Lee royle...@gmail.com wrote: Dear all, I would like to simulate my protein in a lipid bilayer using gromacs 4.5.4, and a forcefield of gromos96. However i don't have the topologies files for lipid bilayer for POPE and DMPE. Anybody knows where can i get the topologies file for POPE and DMPE ? Before that, i had actually used the CHARMM GUI to put my protein into the lipid bilayer. From there, i am not sure how i am able to use the output from CHARMM GUI to do md simulation in gromacs Any help is much appreciated. Thanks a lot! -- 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 -- --- 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] High temperature Simulation
As far as I know we do energy minimization at room temperature only. Only during equilibration (NVT and NPT) we use high temperature for maintaining proper density before starting the final production run. On Mon, Oct 17, 2011 at 15:15, Kavyashree M hmkv...@gmail.com wrote: Dear users, For simulating a protein at high temperature (more than 300K, less than 400K) using OPLSAA forcefield, what are the parameters other than Temperature that need to be taken care of? Does the energy minimization step also needs to be done at high temperature? (here my aim is not to simulate an unfolding event) I have a reference - Biophysical Journal Volume 94 June 2008 –4453 Any other references or suggestions will be helpful. Thanking you With Regards M. Kavyashree -- 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 -- --- 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] High temperature Simulation
Well,as I found in literatures people have used same( 1 atm) pressure at high temperature simulations(NPT simulations). with different water models.As most of the force field parameters are determined generally at 300K and 1 atm. What would be the the possible drawbacks of using the same pressure(or even high pressure) at different temperatures(300K-400K ranges) for a given force field. On Mon, Oct 17, 2011 at 17:04, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Thank you, What about the pressure that need to be used at that temperature (for a system of a protein in tip4p water) The set pressure should reflect whatever system you are trying to model. -Justin Thank you With Regards Kavya On Mon, Oct 17, 2011 at 3:29 PM, bipin singh bipinel...@gmail.com mailto:bipinel...@gmail.com wrote: As far as I know we do energy minimization at room temperature only. Only during equilibration (NVT and NPT) we use high temperature for maintaining proper density before starting the final production run. On Mon, Oct 17, 2011 at 15:15, Kavyashree M hmkv...@gmail.com mailto:hmkv...@gmail.com wrote: Dear users, For simulating a protein at high temperature (more than 300K, less than 400K) using OPLSAA forcefield, what are the parameters other than Temperature that need to be taken care of? Does the energy minimization step also needs to be done at high temperature? (here my aim is not to simulate an unfolding event) I have a reference - Biophysical Journal Volume 94 June 2008 –4453 Any other references or suggestions will be helpful. Thanking you With Regards M. Kavyashree -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- --- Regards, Bipin Singh -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- --- 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] High temperature Simulation
I have not understood what you mean by Energy minimization is (theoretically) at 0 K, as there are no velocities and it is not a true dynamical process. It is clear to me that at 0K there would be no velocities but then why during minimization we expect some conformational rearrangement of side chains etc. On Mon, Oct 17, 2011 at 17:03, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: As far as I know we do energy minimization at room temperature only. Energy minimization is (theoretically) at 0 K, as there are no velocities and it is not a true dynamical process. Only during equilibration (NVT and NPT) we use high temperature for maintaining proper density before starting the final production run. Maintaining density is but one possible goal for NPT; defining the desired ensemble and therefore the sampling distribution is the main reason. -Justin On Mon, Oct 17, 2011 at 15:15, Kavyashree M hmkv...@gmail.com wrote: Dear users, For simulating a protein at high temperature (more than 300K, less than 400K) using OPLSAA forcefield, what are the parameters other than Temperature that need to be taken care of? Does the energy minimization step also needs to be done at high temperature? (here my aim is not to simulate an unfolding event) I have a reference - Biophysical Journal Volume 94 June 2008 –4453 Any other references or suggestions will be helpful. Thanking you With Regards M. Kavyashree -- 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- --- 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] Regarding 1-d free energy profile from g_sham
Hello, I am using g_sham to plot a one dimensional free energy profile for a given reaction coordinate( in my case it is first principal component(PC1) from a principal component analysis). It gives me the bin index Vs free energy plot, but I want PC's value Vs free energy plot. Please suggest me whether it is possible through g_sham or not. -- --- *Thanks and Regards,* Bipin Singh -- --- *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] Regarding 1-d free energy profile from g_sham
Hello, I am using g_sham to plot a one dimensional free energy profile for a given reaction coordinate( in my case it is first principal component(PC1) from a principal component analysis). It gives me the bin index Vs free energy plot, but I want PC's value Vs free energy plot. Please suggest me whether it is possible through g_sham or not. -- --- *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] Identifying representative structures from a g_sham generated 2d energy plot
Hello, Since you already built 2-d free energy landscape (FEL), you should have PCs (PC1 and PC2) as a function of time. You also know from the minima of FEL at which PCs the system spends longer time. Once you find those PCs you should find when the system has those PCs (from PC vs time). Then you should visualize your trajectory and check the structures at those periods of time. Once you collect all the structures you can pick the representative structure. On Fri, Sep 16, 2011 at 15:21, Bailey A. ab...@soton.ac.uk wrote: Hi, Having used g_sham to plot a Gibbs free energy landscape using a projection of the first two principal components from the normal covariance analysis (not dihedral PCA) like so: g_sham -f 2dproj_1_2.xvg -ls gibbs.xpm -notime I would like to now identify which parts of the trajectory are represented by the various parts of the landscape. Are there simple steps to work through to do this? Having looked through the manual, previous user-list correspondence and output files I can see the bins and their contents and cross reference that with the log and ener.xvg, but I got a bit stuck after that. I also had a read of the David Leitner paper from 2007 where they identify structures from dPCA generate plot, “By quenching the structures in the space of the first two dPCA eigenvectors”, but I wasn’t really sure what this means. Any clues to get me started would be much appreciated. Alistair -- 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 -- --- Regards, Bipin Singh IIIT-Hyderabad INDIA -- 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] Representative structure from MD trajectories
Sir, thanks for your reply Yes I should have limited number of structure for a given point(pc1,pc2) but in my case, I have taken pc1 and pc2 as a range of points where the minima in FEL lies rather than a single point.So I think it would be relevant to apply the clustering as per your suggestion.Please let me know whether I am correct or not.. But which clustering method would be better for clustering my MD trajectories is also a question for me. I read some papers in which they have mentioned that the average linkage method works well for most of the cases, is it same to the gromacs linkage method of clustering? Please provide your suggestion. On Sat, Sep 10, 2011 at 13:35, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin, The averages from (2) and (3) are the same and may be far from realistic. Minimizing an average structure may not always yield a structure that is relevant or representative of the ensemble. I would suggest clustering But you should only have a limited number of structures for a given point (pc1,pc2), so why not just visualize the ensemble? Hope it helps, Tsjerk On Sep 10, 2011 8:02 AM, bipin singh bipinel...@gmail.com wrote: Hello, I have constructed a 2-d FEL using PC1 and PC2 as the reaction coordinates(by using g_sham). From this 2-d FEL, I extracted the PC1 and PC2 (principal components) values corresponding to minimum free energy. Then I extracted the time during which system possess these PC's values( by looking at PC Vs time plot). Now I want to extract representative structures from these time length(for eg. 40ns to 70 ns) of MD trajectories. This question had been discussed previously but I am not able to find a consensus solution: There are three approaches discussed in the previous posts: (1)Use g_cluster with options -av(writes average) -cl and then minimize the structure (2)Use g_covar -av, and then minimize the average structure. (3)Use g_rmsf -ox, and minimize the structure Please suggest which approach should be used for this purpose. -- --- Thanks and Regards, Bipin Singh -- 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 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 -- --- Thanks and Regards, Bipin Singh -- --- 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] Regarding clustering of MD data
Sir, thanks for your reply Yes I should have limited number of structure for a given point(pc1,pc2) but in my case, I have taken pc1 and pc2 as a range of points where the minima in FEL lies rather than a single point.So I think it would be relevant to apply the clustering as per your suggestion.Please let me know whether I am correct or not.. But which clustering method would be better for clustering my MD trajectories is also a question for me. I read some papers in which they have mentioned that the average linkage method works well for most of the cases, is it same to the gromacs linkage method of clustering? Please provide your suggestions. On Sat, Sep 10, 2011 at 13:35, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin, The averages from (2) and (3) are the same and may be far from realistic. Minimizing an average structure may not always yield a structure that is relevant or representative of the ensemble. I would suggest clustering But you should only have a limited number of structures for a given point (pc1,pc2), so why not just visualize the ensemble? Hope it helps, Tsjerk On Sep 10, 2011 8:02 AM, bipin singh bipinel...@gmail.com wrote: Hello, I have constructed a 2-d FEL using PC1 and PC2 as the reaction coordinates(by using g_sham). From this 2-d FEL, I extracted the PC1 and PC2 (principal components) values corresponding to minimum free energy. Then I extracted the time during which system possess these PC's values( by looking at PC Vs time plot). Now I want to extract representative structures from these time length(for eg. 40ns to 70 ns) of MD trajectories. This question had been discussed previously but I am not able to find a consensus solution: There are three approaches discussed in the previous posts: (1)Use g_cluster with options -av(writes average) -cl and then minimize the structure (2)Use g_covar -av, and then minimize the average structure. (3)Use g_rmsf -ox, and minimize the structure Please suggest which approach should be used for this purpose. -- --- 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 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] Representative structure from MD trajectories
Hello, I have constructed a 2-d FEL using PC1 and PC2 as the reaction coordinates(by using g_sham). From this 2-d FEL, I extracted the PC1 and PC2 (principal components) values corresponding to minimum free energy. Then I extracted the time during which system possess these PC's values( by looking at PC Vs time plot). Now I want to extract representative structures from these time length(for eg. 40ns to 70 ns) of MD trajectories. This question had been discussed previously but I am not able to find a consensus solution: There are three approaches discussed in the previous posts: (1)Use g_cluster with options -av(writes average) -cl and then minimize the structure (2)Use g_covar -av, and then minimize the average structure. (3)Use g_rmsf -ox, and minimize the structure Please suggest which approach should be used for this purpose. -- --- 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] Representative structure from MD trajectories
Sir, thanks for your reply Yes I should have limited number of structure for a given point(pc1,pc2) but in my case, I have taken pc1 and pc2 as a range of points where the minima in FEL lies rather than a single point.So I think it would be relevant to apply the clustering as per your suggestion.Please let me know whether I am correct or not.. But which clustering method would be better for clustering my MD trajectories is also a question for me. I read some papers in which they have mentioned that the average linkage method works well for most of the cases, is it same to the gromacs linkage method of clustering? Please provide your suggestion. On Sat, Sep 10, 2011 at 13:35, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bipin, The averages from (2) and (3) are the same and may be far from realistic. Minimizing an average structure may not always yield a structure that is relevant or representative of the ensemble. I would suggest clustering But you should only have a limited number of structures for a given point (pc1,pc2), so why not just visualize the ensemble? Hope it helps, Tsjerk On Sep 10, 2011 8:02 AM, bipin singh bipinel...@gmail.com wrote: Hello, I have constructed a 2-d FEL using PC1 and PC2 as the reaction coordinates(by using g_sham). From this 2-d FEL, I extracted the PC1 and PC2 (principal components) values corresponding to minimum free energy. Then I extracted the time during which system possess these PC's values( by looking at PC Vs time plot). Now I want to extract representative structures from these time length(for eg. 40ns to 70 ns) of MD trajectories. This question had been discussed previously but I am not able to find a consensus solution: There are three approaches discussed in the previous posts: (1)Use g_cluster with options -av(writes average) -cl and then minimize the structure (2)Use g_covar -av, and then minimize the average structure. (3)Use g_rmsf -ox, and minimize the structure Please suggest which approach should be used for this purpose. -- --- Thanks and Regards, Bipin Singh -- 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 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 -- --- 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] Regarding xpm2ps
Hello, I am using the below .m2p file as input for xpm2ps, but not able to get axis range label. ; Matrix options titlefont = Helvetica ; Matrix title Postscript Font name titlefontsize = 20.0 ; Matrix title Font size (pt) legend = yes ; Show the legend legendfont = Helvetica ; Legend name Postscript Font name legendfontsize = 12.0 ; Legend name Font size (pt) legendlabel ; Used when there is none in the .xpm legend2label; Id. when merging two xpm's xbox= 0 ; x-size of a matrix element ybox= 0 ; y-size of a matrix element matrixspacing = 20.0 ; Space between 2 matrices xoffset = 0.0 ; Between matrix and bounding box yoffset = 0.0 ; Between matrix and bounding box ; X-axis options x-lineat0value = no; Draw line at matrix value==0 x-major = 4; Major tick spacing x-minor = 2 ; Id. Minor ticks x-firstmajor= 0 ; Offset for major tick x-majorat0 = no; Additional Major tick at first frame x-majorticklen = 8.0 ; Length of major ticks x-minorticklen = 4.0 ; Id. Minor ticks x-label = ; Used when there is none in the .xpm x-font = Helvetica ; Axis label PostScript Font x-fontsize = 12; Axis label Font size (pt) x-tickfont = Helvetica ; Tick label PostScript Font x-tickfontsize = 8 ; Tick label Font size (pt) ;Y-axis options y-lineat0value = no y-major = 4 y-minor = 2 y-firstmajor= 0 y-majorat0 = no y-majorticklen = 8.0 y-minorticklen = 4.0 y-label = y-fontsize = 12 y-font = Helvetica y-tickfontsize = 8 y-tickfont = Helvetica On Wed, Aug 24, 2011 at 00:52, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I have xpm matrix file, for converting this file to ps format I am using xpm2ps e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label mentioned for x and y-axis, in ps file.Please let me know how to set x and y axis range label in ps file. for example I want to set the x and y-axis range from -4 to +4. Use an .m2p file: http://manual.gromacs.org/online/m2p.html -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- --- 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] Regarding xpm2ps
Thanks for your reply, I am attaching the xpm file which I got from g_sham and also attaching the eps output got from xpm2ps.As you can see there is no axis range(PC1 and PC2) labeled in eps file. As the PC1 range is from -4 to +4 and PC2 range from -5 to +4, I want the x-axis range in eps file from -4 to +4(PC1) and y-axis range from -5 to +4(PC2) regardless of the data values in xpm file. But I am unable to get using .m2p file. On Wed, Aug 24, 2011 at 16:22, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I am using the below .m2p file as input for xpm2ps, but not able to get axis range label. What axis range do you obtain? If your data do not actually span from -4 to 4, there's not much you can do. I was assuming you had data that did fit this range. You also didn't say which tool produced the .xpm file; some programs can be forced to adjust the data range, but others can't. -Justin ; Matrix options titlefont = Helvetica ; Matrix title Postscript Font name titlefontsize = 20.0 ; Matrix title Font size (pt) legend = yes ; Show the legend legendfont = Helvetica ; Legend name Postscript Font name legendfontsize = 12.0 ; Legend name Font size (pt) legendlabel ; Used when there is none in the .xpm legend2label ; Id. when merging two xpm's xbox = 0 ; x-size of a matrix element ybox = 0 ; y-size of a matrix element matrixspacing = 20.0 ; Space between 2 matrices xoffset = 0.0 ; Between matrix and bounding box yoffset = 0.0 ; Between matrix and bounding box ; X-axis options x-lineat0value = no ; Draw line at matrix value==0 x-major = 4 ; Major tick spacing x-minor = 2 ; Id. Minor ticks x-firstmajor = 0 ; Offset for major tick x-majorat0 = no ; Additional Major tick at first frame x-majorticklen = 8.0 ; Length of major ticks x-minorticklen = 4.0 ; Id. Minor ticks x-label = ; Used when there is none in the .xpm x-font = Helvetica ; Axis label PostScript Font x-fontsize = 12 ; Axis label Font size (pt) x-tickfont = Helvetica ; Tick label PostScript Font x-tickfontsize = 8 ; Tick label Font size (pt) ;Y-axis options y-lineat0value = no y-major = 4 y-minor = 2 y-firstmajor = 0 y-majorat0 = no y-majorticklen = 8.0 y-minorticklen = 4.0 y-label = y-fontsize = 12 y-font = Helvetica y-tickfontsize = 8 y-tickfont = Helvetica On Wed, Aug 24, 2011 at 00:52, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I have xpm matrix file, for converting this file to ps format I am using xpm2ps e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label mentioned for x and y-axis, in ps file.Please let me know how to set x and y axis range label in ps file. for example I want to set the x and y-axis range from -4 to +4. Use an .m2p file: http://manual.gromacs.org/online/m2p.html -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- --- Regards, Bipin Singh attachment: gibbs.xpm gibbs.eps Description: PostScript document -- 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
Re: [gmx-users] Regarding xpm2ps
Thanks for your kind help, I have tried as per your suggestion, the below command g_sham -f 2d_proj.xvg -xmin -5 -xmax 5 -ls gibbs.xpm It is running without any error , but it is not giving any xpm output... On Wed, Aug 24, 2011 at 17:18, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your reply, I am attaching the xpm file which I got from g_sham and also attaching the eps output got from xpm2ps.As you can see there is no axis range(PC1 and PC2) labeled in eps file. As the PC1 range is from -4 to +4 and PC2 range from -5 to +4, I want the x-axis range in eps file from -4 to +4(PC1) and y-axis range from -5 to +4(PC2) regardless of the data values in xpm file. But I am unable to get using .m2p file. The .m2p file can only be used to adjust axes if the data fit the range you want already. This was unclear from your earlier post. Now that you've said what program you used, we can solve this. g_sham allows you to set the axis manually with the -xmin and -xmax options. Re-run g_sham with these options to set the axes and you should have no problem. -Justin On Wed, Aug 24, 2011 at 16:22, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I am using the below .m2p file as input for xpm2ps, but not able to get axis range label. What axis range do you obtain? If your data do not actually span from -4 to 4, there's not much you can do. I was assuming you had data that did fit this range. You also didn't say which tool produced the .xpm file; some programs can be forced to adjust the data range, but others can't. -Justin ; Matrix options titlefont = Helvetica ; Matrix title Postscript Font name titlefontsize = 20.0 ; Matrix title Font size (pt) legend = yes ; Show the legend legendfont = Helvetica ; Legend name Postscript Font name legendfontsize = 12.0 ; Legend name Font size (pt) legendlabel ; Used when there is none in the .xpm legend2label ; Id. when merging two xpm's xbox = 0 ; x-size of a matrix element ybox = 0 ; y-size of a matrix element matrixspacing = 20.0 ; Space between 2 matrices xoffset = 0.0 ; Between matrix and bounding box yoffset = 0.0 ; Between matrix and bounding box ; X-axis options x-lineat0value = no ; Draw line at matrix value==0 x-major = 4 ; Major tick spacing x-minor = 2 ; Id. Minor ticks x-firstmajor = 0 ; Offset for major tick x-majorat0 = no ; Additional Major tick at first frame x-majorticklen = 8.0 ; Length of major ticks x-minorticklen = 4.0 ; Id. Minor ticks x-label = ; Used when there is none in the .xpm x-font = Helvetica ; Axis label PostScript Font x-fontsize = 12 ; Axis label Font size (pt) x-tickfont = Helvetica ; Tick label PostScript Font x-tickfontsize = 8 ; Tick label Font size (pt) ;Y-axis options y-lineat0value = no y-major = 4 y-minor = 2 y-firstmajor = 0 y-majorat0 = no y-majorticklen = 8.0 y-minorticklen = 4.0 y-label = y-fontsize = 12 y-font = Helvetica y-tickfontsize = 8 y-tickfont = Helvetica On Wed, Aug 24, 2011 at 00:52, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I have xpm matrix file, for converting this file to ps format I am using xpm2ps e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label mentioned for x and y-axis, in ps file.Please let me know how to set x and y axis range label in ps file. for example I want to set the x and y-axis range from -4 to +4. Use an .m2p file: http://manual.gromacs.org/online/m2p.html -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users
Re: [gmx-users] Regarding xpm2ps
Sir, Thanks a lot for your help..Its working... On Wed, Aug 24, 2011 at 18:34, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your kind help, I have tried as per your suggestion, the below command g_sham -f 2d_proj.xvg -xmin -5 -xmax 5 -ls gibbs.xpm It is running without any error , but it is not giving any xpm output... Try with -xmin -5 -5 0 -xmax 5 5 0 - the meaning of the z-axis quantities here has never been clear to me since -gmax should control the range of z-values. Leaving them at zero should cause g_sham to calculate the appropriate range. Otherwise, you're limited to values of z between -5 and 5 also, which may not be appropriate. -Justin On Wed, Aug 24, 2011 at 17:18, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Thanks for your reply, I am attaching the xpm file which I got from g_sham and also attaching the eps output got from xpm2ps.As you can see there is no axis range(PC1 and PC2) labeled in eps file. As the PC1 range is from -4 to +4 and PC2 range from -5 to +4, I want the x-axis range in eps file from -4 to +4(PC1) and y-axis range from -5 to +4(PC2) regardless of the data values in xpm file. But I am unable to get using .m2p file. The .m2p file can only be used to adjust axes if the data fit the range you want already. This was unclear from your earlier post. Now that you've said what program you used, we can solve this. g_sham allows you to set the axis manually with the -xmin and -xmax options. Re-run g_sham with these options to set the axes and you should have no problem. -Justin On Wed, Aug 24, 2011 at 16:22, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I am using the below .m2p file as input for xpm2ps, but not able to get axis range label. What axis range do you obtain? If your data do not actually span from -4 to 4, there's not much you can do. I was assuming you had data that did fit this range. You also didn't say which tool produced the .xpm file; some programs can be forced to adjust the data range, but others can't. -Justin ; Matrix options titlefont = Helvetica ; Matrix title Postscript Font name titlefontsize = 20.0 ; Matrix title Font size (pt) legend = yes ; Show the legend legendfont = Helvetica ; Legend name Postscript Font name legendfontsize = 12.0 ; Legend name Font size (pt) legendlabel ; Used when there is none in the .xpm legend2label ; Id. when merging two xpm's xbox = 0 ; x-size of a matrix element ybox = 0 ; y-size of a matrix element matrixspacing = 20.0 ; Space between 2 matrices xoffset = 0.0 ; Between matrix and bounding box yoffset = 0.0 ; Between matrix and bounding box ; X-axis options x-lineat0value = no ; Draw line at matrix value==0 x-major = 4 ; Major tick spacing x-minor = 2 ; Id. Minor ticks x-firstmajor = 0 ; Offset for major tick x-majorat0 = no ; Additional Major tick at first frame x-majorticklen = 8.0 ; Length of major ticks x-minorticklen = 4.0 ; Id. Minor ticks x-label = ; Used when there is none in the .xpm x-font = Helvetica ; Axis label PostScript Font x-fontsize = 12 ; Axis label Font size (pt) x-tickfont = Helvetica ; Tick label PostScript Font x-tickfontsize = 8 ; Tick label Font size (pt) ;Y-axis options y-lineat0value = no y-major = 4 y-minor = 2 y-firstmajor = 0 y-majorat0 = no y-majorticklen = 8.0 y-minorticklen = 4.0 y-label = y-fontsize = 12 y-font = Helvetica y-tickfontsize = 8 y-tickfont = Helvetica On Wed, Aug 24, 2011 at 00:52, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I have xpm matrix file, for converting this file to ps format I am using xpm2ps e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label mentioned for x and y-axis, in ps file.Please let me know how to set x and y axis range label in ps file. for example I want to set the x and y-axis range from -4 to +4. Use an .m2p file: http://manual.gromacs.org/online/m2p.html -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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
[gmx-users] Regarding xpm2ps
Hello, I have xpm matrix file, for converting this file to ps format I am using xpm2ps e.g: xpm2ps -f file.xpm -o file.eps . But there is no axis range label mentioned for x and y-axis, in ps file.Please let me know how to set x and y axis range label in ps file. for example I want to set the x and y-axis range from -4 to +4. -- --- 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] Regarding g_sham:Please reply
Hello, Please let me know from where can I get the full description of g_sham module, as the manual does not provide full description of the options for g_sham in gromacs. for e.g I want to know the description about the following options in g_sham: -map -ls3 -mdata -- --- 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] Regarding g_sham
Hello, Please let me know from where can I get the full description of g_sham module, as the manual does not provide full description of the options for g_sham in gromacs. for e.g I want to know the description about the following options in g_sham: -map -ls3 -mdata -- --- 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] Regarding g_sham
Thanks for yor reply... I have read manual but there is no description available for the -map -ls3 -mdata options of g_sham On Sat, Aug 13, 2011 at 15:56, lina lina.lastn...@gmail.com wrote: On Sat, Aug 13, 2011 at 3:36 PM, bipin singh bipinel...@gmail.com wrote: Hello, Please let me know from where can I get the full description of g_sham module, as the manual does not provide full description of the options for g_sham in gromacs. for e.g I want to know the description about the following options in g_sham: -map -ls3 -mdata Sorry, I am not sure what's kind of full description you expect, Try: g_sham -h or man g_sham -- --- Regards, Bipin Singh -- 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 -- Best Regards, lina -- 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 -- --- 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] Regarding g_sham
Hello, Please let me know from where can I get the full description of g_sham module, as the manual does not provide full description of the options for g_sham in gromacs. for e.g I want to know the description about the following options in g_sham: -map -ls3 -mdata -- --- 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] PCA and Free energy landscape
Hello, I have done PCA using cartesian coordinates by the help of gromacs(g_covar and g_anaeig), then using the 2-d projection of trajectory on first two eigenvectors as reaction coordinates,I have calculated a 2-d representation of the gibbs free energy landscape(g_sham) using gromacs.Now on this landscape I want to map the conformations(structures from the MD trajectories) of the protein onto the different region(for eg:minima)of this landscape. Please suggest how can I perform this task -- --- 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] Regarding PCA and Gibbs Free energy landscape
Hello, I have done PCA using cartesian coordinates by the help of gromacs(g_covar and g_anaeig), then using the 2-d projection of trajectory on first two eigenvectors as reaction coordinates,I have calculated a 2-d representation of the gibbs free energy landscape using gromacs.Now on this landscape I want to map the conformation(structures from the MD trajectories) of the protein onto the different region(for eg:minima)of this landscape. Please suggest how can I perform this task. -- --- 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] Regarding PCA and FEL
Hello, I have constructed free energy landscape(g_sham) based on the first two principal components, can anyone suggest how to find the representative conformation for a particular region on this 2-d landscape. -- --- 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] Regarding PCA and Free energy landscape
Hello, I have constructed free energy landscape(g_sham) based on the first two principal components, can anyone suggest how to find the representative conformation for a particular region on this 2-d landscape. -- --- 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] Concatenating two trajectories
Hello, I want concatenate two trajectories which have same number of frames and they have written for identical time period i.e. the simulation time is same for both the trajectories(for my case 100ns each) the only thing differ is the temperature of simulation. Please suggest me whether the below commands is right for concatenating these two trajectories: trjcat -f 1.xtc 2.xtc -o concat.xtc -cat -- --- 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] Concatenating two trajectories
Yes It is workingbut I have not tried that, what would be the difference if I don't give -cat option On Wed, Jul 20, 2011 at 16:16, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I want concatenate two trajectories which have same number of frames and they have written for identical time period i.e. the simulation time is same for both the trajectories(for my case 100ns each) the only thing differ is the temperature of simulation. Please suggest me whether the below commands is right for concatenating these two trajectories: trjcat -f 1.xtc 2.xtc -o concat.xtc -cat Presumably. Did you try it? Did it work? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- --- 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] Concatenating two trajectories
Thanks Sir, I understood... On Wed, Jul 20, 2011 at 16:46, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Yes It is workingbut I have not tried that, what would be the difference if I don't give -cat option If the times are the same, then the second trajectory would have overwritten the first. Please read the first paragraph of trjcat -h. -Justin On Wed, Jul 20, 2011 at 16:16, Justin A. Lemkul jalem...@vt.edu wrote: bipin singh wrote: Hello, I want concatenate two trajectories which have same number of frames and they have written for identical time period i.e. the simulation time is same for both the trajectories(for my case 100ns each) the only thing differ is the temperature of simulation. Please suggest me whether the below commands is right for concatenating these two trajectories: trjcat -f 1.xtc 2.xtc -o concat.xtc -cat Presumably. Did you try it? Did it work? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing 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 -- --- 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] which chain to select for MD simulation
Hello, My protein have two identical chains A and B and the backbone rmsd between the two chains is 0.33A. My problem is that how to select(on what basis) one chain out of the two for md simulation, whether the selection of one of the two chains(A or B) will make any differences to the final results. -- --- *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] which chain to select for MD simulation
Sir, You are right..I exactly mean the same as you interpretednow I am clear. Thanks a lot for your reply... On Fri, Jul 8, 2011 at 13:26, felmer...@uchile.cl felmer...@uchile.clwrote: Hey, I agree it was unclear, but i guess he meant that he has a crystal structure with two molecules in the asymmetric unit where he knows that the protein is a monomer in solution. Otherwise the question does not even make sense as you pointed out. If it is indeed the asymmetric unit thing, then of course starting from any of the two structures will give different resultsas they are two different startinf points. However, on the long term all the system properties should converge on the average. Anyways, you should obtain very similar results from any of the two structures. regards Felipe Mensaje original De: mark.abra...@anu.edu.au Fecha: 08-jul-2011 3:44 Para: Discussion list for GROMACS usersgmx-users@gromacs.org Asunto: Re: [gmx-users] which chain to select for MD simulation On 8/07/2011 4:52 PM, bipin singh wrote: Hello, My protein have two identical chains A and B and the backbone rmsd between the two chains is 0.33A. My problem is that how to select(on what basis) one chain out of the two for md simulation, whether the selection of one of the two chains(A or B) will make any differences to the final results. Step back. Does it even make sense to use only one? Dimers are usually that way for a reason. 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 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 -- --- *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
