Re: [gmx-users] spatial distribution function
On 6/17/12 7:56 AM, delara aghaie wrote: Dear Gromacs users. I have simulated a single chain protein in water for 5 ns. Now I want to calculate spatial distribution function. To do this I use command g_spatial. I have read manual for that. I need to have an index group containing the atoms around which the SDF is wanted. It is not clear to me, which atoms to use for such an analysis. It is better to calculate SDF of solvent or protein? which one is more informative? any suggestions would be greatly appreciated There is no absolute way to say anything about which is better. You should be choosing your analysis based on what you want to measure or observe. An SDF for a protein and an SDF for solvent will be wildly different quantities. -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
[gmx-users] spatial distribution function
Dear Gromacs users. I have simulated a single chain protein in water for 5 ns. Now I want to calculate spatial distribution function. To do this I use command g_spatial. I have read manual for that. I need to have an index group containing the atoms around which the SDF is wanted. It is not clear to me, which atoms to use for such an analysis. It is better to calculate SDF of solvent or protein? which one is more informative? any suggestions would be greatly appreciated Regards D.M -- 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] spatial distribution function
I am trying to calculate spatial distribution function (SDF) for ionic liquid.I want to see the distribution of anion around cation. I followed the steps given in gromacs manual.I created two groups each of single cation and all anions in the index file and did two steps trjconv_d to get trajectory for centered solute by removing translational and rotational degrees of freedom. When I am running g_spatial_d on this trajectory I am only able to see anions in my cube file as I am selecting anions for writing output co-ordinates. Am I following correctly or doing something wrong ? I am using updated gromacs version 4.5.4. Please I would really appreciate if someone can help this? Thank you in advance. Pre --- Begin Message --- Hello everyone, I am trying to calculate spatial distribution function (SDF) for ionic liquid.I want to see the distribution of anion around cation. I followed the steps given in gromacs manual.I created two groups each of single cation and all anions in the index file and did two steps trjconv_d to get trajectory for centered solute by removing translational and rotational degrees of freedom. When I am running g_spatial_d on this trajectory I am only able to see anions in my cube file as I am selecting anions for writing output co-ordinates. Am I following correctly or doing something wrong ? I am using updated gromacs version 4.5.4. Please I would really appreciate if someone can help this? Thank you in advance. Prema. --- End Message --- -- 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] spatial distribution function in a binary solvent mixture
Here's the totally wasteful way for you to get what you want: 1. for each molecule in type A: trjorder everything around that molecule and output only the closest N atoms of type A and the closest M atoms of type B. Ensure that the coordinate order is: your central molecule of type A is first, the remaining type A second, and the type B third. 2. concatenate all of these trajectories into one single large trajectory 3. trjconv -fit trans+rot , fitting only to the single central molecule. 4a. g_spatial for the non-central type A 4b. g_spatial for type B * now repeat switching types A and B in the above steps to get the SDFs arouns type B. A much better idea is for you to modify g_spatial to do this all within one loop. But if you don't know C then you are out of luck there. g_sdf may not work because you are underdetermined (there is a symmetry about the long axis that you can not specify). But perhaps you could use that to your advantage and select some totally unrelated atom as the third atom for the fit. My best guess is that this would be no worse than g_spatial. A final option is for you to use g_mindist to output all of the contacts and then run over that with your own script to process the data into an SDF and output it in cube format. Chris. -- original message -- Thanks Chris. I presume g_sdf won't be helpful for my system. [Hide Quoted Text] I think that you have a misconception about what g_spatial does. For a system with many type A and many type B, you need to average over all of one type as the central solute to compute an rdf, and perhaps that is what you want for your sdf. g_spatial, however, does not do any fitting. g_sdf did that. You can obtain an old version of the source (4.0.7 should have it I think) if you want to use g_sdf. I have never used g_sdf myself. In case that doesn't answer your question, then let me make one more point: g_spatial requires that a bin exists for every count. Thus either (a) find a large memory node somewhere or (b) pre-process your trajectory using trjorder to order the solvent molecules and then keep only the N closest, then run g_spatial. But again, I think that this will not provide what you are looking for but is likely to give you a smear over your box. Chris. -- original message -- Dear all, I'm working with a binary solvent mixture containing 2000 molecules (1800 type-A + 200 type-B). Both the types of solvent molecules have similar structure (they are both diatomic molecules) except the polarity.I'm trying to calculate sdf of type-B solvent molecules. I followed the step-by-step instructions from the manual using g_spatial. I'm trying to reduce the bin width to 0.05A. The *.cube file generated with a bin width of 0.09A is already 4.9GB in size. As I'm more interested in the first solvation shell around the type-B solvent molecule, I was wondering if I could find a way to control the maximum radius of the sphere around central molecule (center of coordinates?)? Also, can anyone please let me know how g_spatial deals with the angular part of sdf? (I've searched a lot but could not gather enough meaningful information) regards, Debasmita -- 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] spatial distribution function in a binary solvent mixture
Thanks Chris. I presume g_sdf won't be helpful for my system. > I think that you have a misconception about what g_spatial does. For a > system with many type A and many type B, you need to average over all > of one type as the central solute to compute an rdf, and perhaps that > is what you want for your sdf. g_spatial, however, does not do any > fitting. g_sdf did that. You can obtain an old version of the source > (4.0.7 should have it I think) if you want to use g_sdf. I have never > used g_sdf myself. > > In case that doesn't answer your question, then let me make one more > point: > > g_spatial requires that a bin exists for every count. Thus either (a) > find a large memory node somewhere or (b) pre-process your trajectory > using trjorder to order the solvent molecules and then keep only the N > closest, then run g_spatial. But again, I think that this will not > provide what you are looking for but is likely to give you a smear > over your box. > > Chris. > > -- original message -- > >Dear all, > > I'm working with a binary solvent mixture containing 2000 molecules > (1800 > type-A + 200 type-B). Both the types of solvent molecules have similar > structure (they are both diatomic molecules) except the polarity.I'm > trying to calculate sdf of type-B solvent molecules. I followed the > step-by-step instructions from the manual using g_spatial. > I'm trying to reduce the bin width to 0.05A. The *.cube file generated > with a bin width of 0.09A is already 4.9GB in size. As I'm more > interested in the first solvation shell around the type-B solvent > molecule, I was wondering if I could find a way to control the maximum > radius of the sphere around central molecule (center of coordinates?)? > Also, can anyone please let me know how g_spatial deals with the angular > part of sdf? > > (I've searched a lot but could not gather enough meaningful information) > > regards, > Debasmita > > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] spatial distribution function in a binary solvent mixture
I think that you have a misconception about what g_spatial does. For a system with many type A and many type B, you need to average over all of one type as the central solute to compute an rdf, and perhaps that is what you want for your sdf. g_spatial, however, does not do any fitting. g_sdf did that. You can obtain an old version of the source (4.0.7 should have it I think) if you want to use g_sdf. I have never used g_sdf myself. In case that doesn't answer your question, then let me make one more point: g_spatial requires that a bin exists for every count. Thus either (a) find a large memory node somewhere or (b) pre-process your trajectory using trjorder to order the solvent molecules and then keep only the N closest, then run g_spatial. But again, I think that this will not provide what you are looking for but is likely to give you a smear over your box. Chris. -- original message -- Dear all, I'm working with a binary solvent mixture containing 2000 molecules (1800 type-A + 200 type-B). Both the types of solvent molecules have similar structure (they are both diatomic molecules) except the polarity.I'm trying to calculate sdf of type-B solvent molecules. I followed the step-by-step instructions from the manual using g_spatial. I'm trying to reduce the bin width to 0.05A. The *.cube file generated with a bin width of 0.09A is already 4.9GB in size. As I'm more interested in the first solvation shell around the type-B solvent molecule, I was wondering if I could find a way to control the maximum radius of the sphere around central molecule (center of coordinates?)? Also, can anyone please let me know how g_spatial deals with the angular part of sdf? (I've searched a lot but could not gather enough meaningful information) regards, Debasmita -- 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] spatial distribution function in a binary solvent mixture
Dear all, I'm working with a binary solvent mixture containing 2000 molecules (1800 type-A + 200 type-B). Both the types of solvent molecules have similar structure (they are both diatomic molecules) except the polarity.I'm trying to calculate sdf of type-B solvent molecules. I followed the step-by-step instructions from the manual using g_spatial. I'm trying to reduce the bin width to 0.05A. The *.cube file generated with a bin width of 0.09A is already 4.9GB in size. As I'm more interested in the first solvation shell around the type-B solvent molecule, I was wondering if I could find a way to control the maximum radius of the sphere around central molecule (center of coordinates?)? Also, can anyone please let me know how g_spatial deals with the angular part of sdf? (I've searched a lot but could not gather enough meaningful information) regards, Debasmita -- 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] spatial distribution function for ionic liquid
Dear all... I want to get spatial distribution function for ionic liquid. So, I used g_sdf command as below g_sdf -f mixture_mdpr.trr -n index.ndx -s mixture_mdpr.tpr -o sdf_plt.dat -r sdf.gro -mode 1 -grid 3.8 3.8 3.8 I rename the output file from .dat file to .plt file and I used VMD to view the 3-D structure. The 3-D structure seems like not correct... The ionic liquid that I use is tetraethylammonium L-glutaminate.. I already create 4 group for index file. The first three groups comes from cation which is [C04], [C06] and [C08] and the last group, which is group 4 comes from anion. [ C04 ] 2201 [ C06 ] 2185 [ C08 ] 2192 [ ANION ] 4405 4406 4407 4408 4409 4410 4411 4412 4413 4414 4415 4416 4417 4418 4419 4420 4421 4422 4423 4671 4672 4673 4674 4675 4676 4677 4678 4679 4680 4681 4682 4683 4684 4685 4686 4687 4688 4689 4823 4824 4825 4826 4827 4828 4829 4830 4831 4832 4833 4834 4835 4836 4837 4838 4839 4840 4841 5051 5052 5053 5054 5055 5056 5057 5058 5059 5060 5061 5062 5063 5064 5065 5066 5067 5068 5069 5203 5204 5205 5206 5207 5208 5209 5210 5211 5212 5213 5214 5215 5216 5217 5218 5219 5220 5221 5222 5223 5224 5225 5226 5227 5228 5229 5230 5231 5232 5233 5234 5235 5236 5237 5238 5239 5240 5241 5242 5243 5244 5245 5246 5247 5248 5249 5250 5251 5252 5253 5254 5255 5256 5257 5258 5259 My question is, 1) which -mode that i should used to get the probability density anion around cation in g_sdf? 2) Could anybody tell me what is the different between -mode 1, -mode 2 and -mode 3 in g_sdf? 3) what -mode is suitable for my ionic liquid? Thanks IMA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] spatial distribution function (SDF)
First three groups are the reference group, from which the SDF is generated, it sets the coordinate system. That means you need to have at least three "atoms" in the "molecule" you are generating the SDF from. Catch ya, Dr Dallas Warren Pharmacy and Pharmaceutical Sciences Monash University A polar bear is a Cartesian bear that has undergone a polar transformation -Original Message- From: gmx-users-boun...@gromacs.org on behalf of naimah haron naimah Sent: Thu 12/3/2009 9:03 PM To: gromacs Subject: [gmx-users] spatial distribution function (SDF) Hai all... Did anyone know how to do spatial distribution functions??? I have 125 ion pairs in my system. The problem is, 1)how I can I get the 3-D probability distributions of anion around cation or cation around anion in my system? Could anybody tell me the method? 2)When I read the GROMACS manual, I should create 4 group in my index file. Can anybody tell me what is first, second, three and for group represent??? I already try to do it, but I'm failed to get the result.. Thanks IMA <>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] spatial distribution function (SDF)
g_spatial -h -or- g_sdf -h -- original message -- ai all... Did anyone know how to do spatial distribution functions??? I have 125 ion pairs in my system. The problem is, 1)how I can I get the 3-D probability distributions of anion around cation or cation around anion in my system? Could anybody tell me the method? 2)When I read the GROMACS manual, I should create 4 group in my index file. Can anybody tell me what is first, second, three and for group represent??? I already try to do it, but I'm failed to get the result.. Thanks IMA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] spatial distribution function (SDF)
Hai all... Did anyone know how to do spatial distribution functions??? I have 125 ion pairs in my system. The problem is, 1)how I can I get the 3-D probability distributions of anion around cation or cation around anion in my system? Could anybody tell me the method? 2)When I read the GROMACS manual, I should create 4 group in my index file. Can anybody tell me what is first, second, three and for group represent??? I already try to do it, but I'm failed to get the result.. Thanks IMA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Spatial distribution
I am not sure what is going on in this case. You could try: which g_spatial to see what is being picked up. You could also try to move the g_spatial executable to its own directory and then execute g_spatial from that path: /new/path/to/executable/g_spatial -h ls /new/path/to/executable/g_spatial g_spatial Otherwise I am not sure what is going on. Are you sure that you didn't compile g_cluster under the name g_spatial by accident? Chris. -- original message -- HI Chris I followed the steps below and when i tried to run g_spatial it executed g_cluster instead. Even when i do g_spatial -h it looks like its being overwritten by g_cluster 1.I used make_ndx to create a group containing the atoms around which i want the SDF 2. trjconv -s md.tpr -f tyrc_md.trr -o tyrc1.xtc -center tric -ur compact -pbc none 3. trjconv -s md.tpr -f tyrc1.xtc -o tyrc2.xtc -fit rot+trans 4. g_spatial -s md.tpr -f tyrc2.xtc -n index.ndx ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Spatial distribution
HI Chris I followed the steps below and when i tried to run g_spatial it executed g_cluster instead. Even when i do g_spatial -h it looks like its being overwritten by g_cluster 1.I used make_ndx to create a group containing the atoms around which i want the SDF 2. trjconv -s md.tpr -f tyrc_md.trr -o tyrc1.xtc -center tric -ur compact -pbc none 3. trjconv -s md.tpr -f tyrc1.xtc -o tyrc2.xtc -fit rot+trans 4. g_spatial -s md.tpr -f tyrc2.xtc -n index.ndx I wrote g_spatial and it should produce a spatial distribution function. However, it's rather complicated to use. Did you follow the directions in g_spatial -h ? There are about 10 steps to use it. It is so complicated on purpose in order to give the user full flexibility, but this means that you need to do all of your alignment yourself. If you did that correctly, then I also suggest that you should make sure that you are visualizing it correctly in VMD. By default you will see some atoms, but that is only there because VMD will not recognize a gaussian cube without any atoms, and also it makes it easier for you to ensure that any other pdbs you may load overlay correctly. Therefore ensure that you switch the representation to isosurface and then slide the bar so that you see the appropriate isosurface contour. Please report back to the list with findings so that other users can later benifit from your work Chris. Gadzikano Munyuki wrote: > I want to analyse the solvent around a peptide . I used g_sdf and > the output that i am getting (i.e the refmol.gro) does not have the > whole peptide molecule but just the residues that i use to define > the coordinate system . I then tried to use g_spatialbut its doing > something very different and not spatial distibution, it looks like > its executing g_cluster instead. I was wondering if g_custer and > g_spatial are meant to do the same thing. Have a read of g_cluster -h and g_spatial -h and decide whether they're doing the same thing :-) Mark __ UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 4500. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. _ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Spatial distribution
I wrote g_spatial and it should produce a spatial distribution function. However, it's rather complicated to use. Did you follow the directions in g_spatial -h ? There are about 10 steps to use it. It is so complicated on purpose in order to give the user full flexibility, but this means that you need to do all of your alignment yourself. If you did that correctly, then I also suggest that you should make sure that you are visualizing it correctly in VMD. By default you will see some atoms, but that is only there because VMD will not recognize a gaussian cube without any atoms, and also it makes it easier for you to ensure that any other pdbs you may load overlay correctly. Therefore ensure that you switch the representation to isosurface and then slide the bar so that you see the appropriate isosurface contour. Please report back to the list with findings so that other users can later benifit from your work Chris. Gadzikano Munyuki wrote: I want to analyse the solvent around a peptide . I used g_sdf and the output that i am getting (i.e the refmol.gro) does not have the whole peptide molecule but just the residues that i use to define the coordinate system . I then tried to use g_spatialbut its doing something very different and not spatial distibution, it looks like its executing g_cluster instead. I was wondering if g_custer and g_spatial are meant to do the same thing. Have a read of g_cluster -h and g_spatial -h and decide whether they're doing the same thing :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Spatial distribution
Gadzikano Munyuki wrote: I want to analyse the solvent around a peptide . I used g_sdf and the output that i am getting (i.e the refmol.gro) does not have the whole peptide molecule but just the residues that i use to define the coordinate system . I then tried to use g_spatialbut its doing something very different and not spatial distibution, it looks like its executing g_cluster instead. I was wondering if g_custer and g_spatial are meant to do the same thing. Have a read of g_cluster -h and g_spatial -h and decide whether they're doing the same thing :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Spatial distribution
I want to analyse the solvent around a peptide . I used g_sdf and the output that i am getting (i.e the refmol.gro) does not have the whole peptide molecule but just the residues that i use to define the coordinate system . I then tried to use g_spatialbut its doing something very different and not spatial distibution, it looks like its executing g_cluster instead. I was wondering if g_custer and g_spatial are meant to do the same thing. Gadzikano __ UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 4500. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. _ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
