Re: [gmx-users] Docking with PyMol and using Gromacs
Dallas B. Warren a écrit : Coordinate files like pdb and gro aren’t used by GROMACS to provide any bonding information. That is what the topology files are for. So their “presence” in your pdb isn’t an issue. Actually, what is probably happening is that PyMol is guessing the bonds presence, based on the distance between atoms, and displaying it (which is what VMD does as well). So the bonds aren’t actually there at all in the pdb file. VMD can read/write CHARMM/NAMD topology files (namely psf files). If your problem is *just* a visualization artefact, you can load your structure in VMD, write a psf file and delete the unwanted bonds (this does not require a specific forcefield). You can also combine 2 psf files (1 for your protein and 1 for your ligand), that require some basic knowledge of TCL though. After that, you just have to load the topology abd the coordinates: vmd -psf topology.psf -pdb coordinate.pdb You won't see any weird bonds. Nicolas Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Gunnar Widtfeldt Reginsson *Sent:* Thursday, 12 November 2009 10:13 AM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Docking with PyMol and using Gromacs Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as one pdb file and the organic molecule as another pdb file. I open the DNA file in pymol and then load the organic molecule. After docking the organic molecule I write "save name.pdb" When viewing the name.pdb file in pymol there are some bonds between the organic molecule and the DNA that I don't want. Somehow pymol creates them and I don't see those bonds in the name.pdb file when I open it in a text reader. I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file of the organic molecule with topolbuilder 1.2 , and unite those .gro files and convert into a .pdb with editconf The newly created pdb file still has those unwanted bonds. My question is: Can I ignore those bonds? If not, how can I prevent pymol making those bonds? Thanks. <>-- 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] Docking with PyMol and using Gromacs
With VMD it's even simpler: use "dynamic bonds". Ran. Nicolas Sapay wrote: > > > Dallas B. Warren a écrit : >> >> Coordinate files like pdb and gro aren’t used by GROMACS to provide >> any bonding information. That is what the topology files are for. So >> their “presence” in your pdb isn’t an issue. >> >> Actually, what is probably happening is that PyMol is guessing the >> bonds presence, based on the distance between atoms, and displaying >> it (which is what VMD does as well). So the bonds aren’t actually >> there at all in the pdb file. >> > VMD can read/write CHARMM/NAMD topology files (namely psf files). If > your problem is *just* a visualization artefact, you can load your > structure in VMD, write a psf file and delete the unwanted bonds (this > does not require a specific forcefield). You can also combine 2 psf > files (1 for your protein and 1 for your ligand), that require some > basic knowledge of TCL though. After that, you just have to load the > topology abd the coordinates: > >vmd -psf topology.psf -pdb coordinate.pdb > > You won't see any weird bonds. > > Nicolas >> >> Catch ya, >> >> Dr. Dallas Warren >> Drug Delivery, Disposition and Dynamics >> Monash Institute of Pharmaceutical Sciences, Monash University >> 381 Royal Parade, Parkville VIC 3010 >> dallas.war...@pharm.monash.edu.au >> +61 3 9903 9167 >> - >> When the only tool you own is a hammer, every problem begins to >> resemble a nail. >> >> *From:* gmx-users-boun...@gromacs.org >> [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Gunnar >> Widtfeldt Reginsson >> *Sent:* Thursday, 12 November 2009 10:13 AM >> *To:* gmx-users@gromacs.org >> *Subject:* [gmx-users] Docking with PyMol and using Gromacs >> >> Hi. >> >> I am a new user of Gromacs. >> >> My question is both PyMol and Gromacs related. >> >> I tried the PyMol users mailing list but couldn't find anything. >> >> I have a small organic molecule that I am inserting into DNA in pymol. >> >> I have the DNA as one pdb file and the organic molecule as another >> pdb file. I open the DNA file in pymol and then load the organic >> molecule. After docking the organic molecule I write "save name.pdb" >> >> When viewing the name.pdb file in pymol there are some bonds between >> the organic molecule and the DNA that I don't want. Somehow pymol >> creates them and I don't see those bonds in the name.pdb file when I >> open it in a text reader. >> >> I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file >> of the organic molecule with topolbuilder 1.2 , and unite those .gro >> files and convert into a .pdb with editconf >> >> The newly created pdb file still has those unwanted bonds. >> >> My question is: >> >> Can I ignore those bonds? >> >> If not, how can I prevent pymol making those bonds? >> >> Thanks. >> -- 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] membrane protein tutorial information
Dear all, I am busy following the EMBO tutorial on membrane proteins (http://www.dddc.ac.cn/embo04/practicals/9_16.htm) but it is 2 days now that the server is down. Does anybody maybe know another url where I can find this tutorial? Thanks! Irene -- 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] LJ scaling and EnerPress correction
> > I am trying to simulate a two component system, and I would like to ask > > you the two following questions: > > > > 1) Is it possible to use a different scaling factor (for the LJ and the > > electrostatics) for each component? > > Not natively. How would you like to treat non-bonded interactions > between atoms belonging to different components? I am still trying to figure that out. According to the force fields I am using for the bulk systems of the two components are applying different scaling factors. > > 2) Is it possible to use energy and pressure correction only for the one > > of the two components and not for the other? > > No. Why would you want to do this? Because the force fields that I am using to describe my two-component system, are different in this aspect. The one of them was "designed" using energy and pressure correction and the other one not. Thank you for your reply Antonia _ Windows Live: Make it easier for your friends to see what you’re up to on Facebook. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_2:092009-- 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] Docking with PyMol and using Gromacs
This is exactly what I thought. I found out that saving the file with .mol ending in PyMol does not give the unwanted bonds. Thank you all. On Thu, Nov 12, 2009 at 8:49 AM, Ran Friedman wrote: > With VMD it's even simpler: use "dynamic bonds". > > Ran. > > Nicolas Sapay wrote: > > > > > > Dallas B. Warren a écrit : > >> > >> Coordinate files like pdb and gro aren’t used by GROMACS to provide > >> any bonding information. That is what the topology files are for. So > >> their “presence” in your pdb isn’t an issue. > >> > >> Actually, what is probably happening is that PyMol is guessing the > >> bonds presence, based on the distance between atoms, and displaying > >> it (which is what VMD does as well). So the bonds aren’t actually > >> there at all in the pdb file. > >> > > VMD can read/write CHARMM/NAMD topology files (namely psf files). If > > your problem is *just* a visualization artefact, you can load your > > structure in VMD, write a psf file and delete the unwanted bonds (this > > does not require a specific forcefield). You can also combine 2 psf > > files (1 for your protein and 1 for your ligand), that require some > > basic knowledge of TCL though. After that, you just have to load the > > topology abd the coordinates: > > > >vmd -psf topology.psf -pdb coordinate.pdb > > > > You won't see any weird bonds. > > > > Nicolas > >> > >> Catch ya, > >> > >> Dr. Dallas Warren > >> Drug Delivery, Disposition and Dynamics > >> Monash Institute of Pharmaceutical Sciences, Monash University > >> 381 Royal Parade, Parkville VIC 3010 > >> dallas.war...@pharm.monash.edu.au > >> +61 3 9903 9167 > >> - > >> When the only tool you own is a hammer, every problem begins to > >> resemble a nail. > >> > >> *From:* gmx-users-boun...@gromacs.org > >> [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Gunnar > >> Widtfeldt Reginsson > >> *Sent:* Thursday, 12 November 2009 10:13 AM > >> *To:* gmx-users@gromacs.org > >> *Subject:* [gmx-users] Docking with PyMol and using Gromacs > >> > >> Hi. > >> > >> I am a new user of Gromacs. > >> > >> My question is both PyMol and Gromacs related. > >> > >> I tried the PyMol users mailing list but couldn't find anything. > >> > >> I have a small organic molecule that I am inserting into DNA in pymol. > >> > >> I have the DNA as one pdb file and the organic molecule as another > >> pdb file. I open the DNA file in pymol and then load the organic > >> molecule. After docking the organic molecule I write "save name.pdb" > >> > >> When viewing the name.pdb file in pymol there are some bonds between > >> the organic molecule and the DNA that I don't want. Somehow pymol > >> creates them and I don't see those bonds in the name.pdb file when I > >> open it in a text reader. > >> > >> I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file > >> of the organic molecule with topolbuilder 1.2 , and unite those .gro > >> files and convert into a .pdb with editconf > >> > >> The newly created pdb file still has those unwanted bonds. > >> > >> My question is: > >> > >> Can I ignore those bonds? > >> > >> If not, how can I prevent pymol making those bonds? > >> > >> Thanks. > >> > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Constraints & Restraints
Mark Abraham skrev: Darrell Koskinen wrote: Hi Tsjerk, So then, if I understand correctly, setting "constraints = all-bonds" is not as realistic as setting "constraints = none", since the latter will allow for flexible (e.g. harmonic) behavoir which is more realistic than fixing the bond to a certain distance, correct? Actually not. It would be a better model of a harmonic potential (duh), but it has been shown that the use of constraints can lead to a (more?) acceptable model of a real system, and they allow a larger integration time to boot. Check out the papers for the constraint algorithms (refs in GROMACS manual). Mark Agreed. And this is especially true for hydrogen atoms as I understand it, since their behaviour as quantum particles deviate more from a classical treatment than is the case for heavier nuclei. This is mentioned in the gromacs manual. /Erik Date: Wed, 11 Nov 2009 21:45:44 +0100 From: Tsjerk Wassenaar Subject: Re: [gmx-users] Constraints & Restraints To: Discussion list for GROMACS users Message-ID: <8ff89815091245u63c6aa65sa839f24634352...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Darrell, Constraints and restraints also apply to relative positions. A bond constraint fixes the bond to a certain distance. constraints = all-bonds means that all bonds are to be converted to constraints, rather than have them flexible, e.g. harmonic. Harmonic bonds are actually more like restraints, penalizing deviations from the equilibrium values. These equilibrium values and the 'penalty function' are described in the force field. Hope it helps, Tsjerk On Wed, Nov 11, 2009 at 9:32 PM, wrote: Hi, I just have a quick question on contraints and restraints. My understanding is that "constraints" fix the position of an atom in space and "restraints" restrain the deviation of the atom's position from its equilibrium point. Is that correct? If so, then I am a little confused by the purpose of "constraints = all-bonds" or "constraints = none" in an mdp file, since by selection of a force field, which has bond/angle/dihedral stretching/bending/torsion constants, we are specifying the constraints applied to the simulation. So then what is the purpose of "constraints = all-bonds" and "constraints = none"? Thanks. Darrell -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- 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] LJ scaling and EnerPress correction
Antonia V. wrote: > > I am trying to simulate a two component system, and I would like to ask > > you the two following questions: > > > > 1) Is it possible to use a different scaling factor (for the LJ and the > > electrostatics) for each component? > > Not natively. How would you like to treat non-bonded interactions > between atoms belonging to different components? I am still trying to figure that out. According to the force fields I am using for the bulk systems of the two components are applying different scaling factors. > > 2) Is it possible to use energy and pressure correction only for the one > > of the two components and not for the other? > > No. Why would you want to do this? Because the force fields that I am using to describe my two-component system, are different in this aspect. The one of them was "designed" using energy and pressure correction and the other one not. So that brings us to the heart of the matter :-) Mixing forcefields is a bad idea unless you can prove it works. See http://www.gromacs.org/Documentation/Terminology/Force_Fields Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Constraints & Restraints
Erik Marklund wrote: > Mark Abraham skrev: >> Darrell Koskinen wrote: >>> Hi Tsjerk, >>> So then, if I understand correctly, setting "constraints = >>> all-bonds" is not as realistic as setting "constraints = none", >>> since the latter will allow for flexible (e.g. harmonic) behavoir >>> which is more realistic than fixing the bond to a certain distance, >>> correct? >> >> Actually not. It would be a better model of a harmonic potential >> (duh), but it has been shown that the use of constraints can lead to >> a (more?) acceptable model of a real system, and they allow a larger >> integration time to boot. Check out the papers for the constraint >> algorithms (refs in GROMACS manual). >> >> Mark >> > Agreed. And this is especially true for hydrogen atoms as I understand > it, since their behaviour as quantum particles deviate more from a > classical treatment than is the case for heavier nuclei. This is > mentioned in the gromacs manual. > > /Erik This depends on the system you study. In some cases it is necessary not to constrain the hydrogen atoms to get a better agreement with the experiment. Also, if one needs to deal with vibrational spectra involving hydrogens, they must be mobile. Ran. Date: Wed, 11 Nov 2009 21:45:44 +0100 From: Tsjerk Wassenaar Subject: Re: [gmx-users] Constraints & Restraints To: Discussion list for GROMACS users Message-ID: <8ff89815091245u63c6aa65sa839f24634352...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Darrell, Constraints and restraints also apply to relative positions. A bond constraint fixes the bond to a certain distance. constraints = all-bonds means that all bonds are to be converted to constraints, rather than have them flexible, e.g. harmonic. Harmonic bonds are actually more like restraints, penalizing deviations from the equilibrium values. These equilibrium values and the 'penalty function' are described in the force field. Hope it helps, Tsjerk On Wed, Nov 11, 2009 at 9:32 PM, wrote: > Hi, > I just have a quick question on contraints and restraints. My > understanding is that "constraints" fix the position of an atom in > space and "restraints" restrain the deviation of the atom's position > from its equilibrium point. Is that correct? If so, then I am a > little > confused by the purpose of "constraints = all-bonds" or "constraints > = none" in an mdp file, since by selection of a force field, which > has > bond/angle/dihedral stretching/bending/torsion constants, we are > specifying the constraints applied to the simulation. So then what is > the purpose of "constraints = all-bonds" and "constraints = none"? > > Thanks. > > Darrell > > > -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman -- -- 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] Hydrogen bond occupancy for the dimer of Acetic Acid
Hi All. I'm trying to calculate the Hydrogen bond occupancy when there is two hydrogen bonds between same two acetic acid molecules at the same time. With g_hbond I can get the hbond.ndx giving me "all ocuring hydrogen bonds" group and the hbmap.xpm gives me the matrix of when these hydrogen bonds exist for each timeframe... How can I calculate the occupancy of when two hydrogen bonds exist between the same two molecules?? Best regards Rasmus -- 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] Hydrogen bond occupancy for the dimer of Acetic Acid
Hi Rasmus, A simple solution would be to run g_hbond twice, with two separate groups for acetate 1 as donor and acetate 2 as acceptor or vice versa, check the existence an hydrogen bond with g_hbond -num and write a script to check when the two hydrogen bonds co-exist. Hope that helps, Ran. Rasmus "Termo" Lundsgaard wrote: > Hi All. > > I'm trying to calculate the Hydrogen bond occupancy when there is two > hydrogen bonds between same two acetic acid molecules at the same time. > > With g_hbond I can get the hbond.ndx giving me "all ocuring hydrogen > bonds" group and the hbmap.xpm gives me the matrix of when these > hydrogen bonds exist for each timeframe... > > How can I calculate the occupancy of when two hydrogen bonds exist > between the same two molecules?? > > > Best regards > Rasmus -- 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] Hydrogen bond occupancy for the dimer of Acetic Acid
Hi Ran. If I understand you right, then you suggest to have one molecule as acceptor, and the rest (499) as donors, and then look in the hbnum.xvg to see how often there is two hydrogen bonds... 1. is that I have to do this check for every molecule. 2. there is no guaranty that the two hydrogen bonds are to the same other molecule - it could very well be as a part of a chain... 3. If possible I would like to do measurement of distance between molecules when they are bonded as a dimer... Best regards Rasmus Ran Friedman wrote: Hi Rasmus, A simple solution would be to run g_hbond twice, with two separate groups for acetate 1 as donor and acetate 2 as acceptor or vice versa, check the existence an hydrogen bond with g_hbond -num and write a script to check when the two hydrogen bonds co-exist. Hope that helps, Ran. Rasmus "Termo" Lundsgaard wrote: Hi All. I'm trying to calculate the Hydrogen bond occupancy when there is two hydrogen bonds between same two acetic acid molecules at the same time. With g_hbond I can get the hbond.ndx giving me "all ocuring hydrogen bonds" group and the hbmap.xpm gives me the matrix of when these hydrogen bonds exist for each timeframe... How can I calculate the occupancy of when two hydrogen bonds exist between the same two molecules?? Best regards Rasmus -- 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] Hydrogen bond occupancy for the dimer of Acetic Acid
Hi Rasmus, >From your previous email I understood that you have only two molecules (you didn't write that you're using 500 and nothing on the rest of the system). Apparently, this is not the case. I don't think you can get what you want from g_hbond without modifying the source code. If you don't mind 500 runs you can use g_dist -dist, where group 1 is a single hydrogen bond donor oxygen and group two all potential acceptors, find the molecules which satisfy your criterion and then run g_hbond on them if you want to be sure that you have a hydrogen bond that satisfy angle criteria as well. Tedious, but can work with some scripting and patience. Ran. Rasmus "Termo" Lundsgaard wrote: > Hi Ran. > > If I understand you right, then you suggest to have one molecule as > acceptor, and the rest (499) as donors, and then look in the hbnum.xvg > to see how often there is two hydrogen bonds... > > 1. is that I have to do this check for every molecule. > > 2. there is no guaranty that the two hydrogen bonds are to the same > other molecule - it could very well be as a part of a chain... > > 3. If possible I would like to do measurement of distance between > molecules when they are bonded as a dimer... > > Best regards > Rasmus > > > Ran Friedman wrote: >> Hi Rasmus, >> >> A simple solution would be to run g_hbond twice, with two separate >> groups for acetate 1 as donor and acetate 2 as acceptor or vice versa, >> check the existence an hydrogen bond with g_hbond -num and write a >> script to check when the two hydrogen bonds co-exist. >> >> Hope that helps, >> Ran. >> >> Rasmus "Termo" Lundsgaard wrote: >> >>> Hi All. >>> >>> I'm trying to calculate the Hydrogen bond occupancy when there is two >>> hydrogen bonds between same two acetic acid molecules at the same time. >>> >>> With g_hbond I can get the hbond.ndx giving me "all ocuring hydrogen >>> bonds" group and the hbmap.xpm gives me the matrix of when these >>> hydrogen bonds exist for each timeframe... >>> >>> How can I calculate the occupancy of when two hydrogen bonds exist >>> between the same two molecules?? >>> >>> >>> Best regards >>> Rasmus >>> >> >> >> > -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman -- -- 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] Density histogram in Ramachandran plot
Hi, I wonder if there is an easy way I am missing to get a density histogram from the Ramachandran plot over a trajectory as outputted by g_rama. All I see are big, uniform black blobs and they're not helpful, because with tons of data points a density plot would be much more informative. Thanks! 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/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] free energy calculation using TI
Dear all, I have a covalently bond ligand to a protein which its c=c bond could stay in Cis-enamine or Trans-enamine (I relaxed the structures of those two using classical MD in Gromacs4). I'm calculating the free energy difference of the Cis and Trans states using thermodynamic integration implemented in Gromacs4. Besides the dihedrals of Cis and Trans that are specified in the topology file (so Gromacs should undersatnd it should rotate around the specific bond gratually), I would like Gromacs consider both Cis and Trans coordinates when it is calculating the potential of mean force. How can I make it accept the two coordinates at the same time? Thanks in advance, Zhaleh -- 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] Constraints & Restraints
Thanks for the additional comments. So given that, in my system, I have H atoms attached to C atoms on the perimeter of a finite graphene sheet that is placed above multiple infinite layers of graphene (graphite), would it be more appropriate to use: (i) a classical (harmonic) model using constraints=none or (ii) a constrained model using constraints=all-bonds? Note that, currently, I use constraints=none and see that the C atoms in the graphene sheet are well behaved and not vibrating very much, but the H atoms on the perimeter are vibrating wildly. Would you have any idea of whether this is natural and to be expected or not? Maybe this is an indication that constraints should be used in this particular model. However, I have no idea whether it is natural for hydrogen atoms to flip and flop around so much on the edge of a graphene sheet. Your comments are appreciated. Darrell Date: Thu, 12 Nov 2009 14:16:06 +0100 From: Ran Friedman Subject: Re: [gmx-users] Constraints & Restraints To: Discussion list for GROMACS users Message-ID: <4afc0a96@bioc.uzh.ch> Content-Type: text/plain; charset=ISO-8859-1 Erik Marklund wrote: > Mark Abraham skrev: >> Darrell Koskinen wrote: >>> Hi Tsjerk, >>> So then, if I understand correctly, setting "constraints = >>> all-bonds" is not as realistic as setting "constraints = none", >>> since the latter will allow for flexible (e.g. harmonic) behavoir >>> which is more realistic than fixing the bond to a certain distance, >>> correct? >> >> Actually not. It would be a better model of a harmonic potential >> (duh), but it has been shown that the use of constraints can lead to >> a (more?) acceptable model of a real system, and they allow a larger >> integration time to boot. Check out the papers for the constraint >> algorithms (refs in GROMACS manual). >> >> Mark >> > Agreed. And this is especially true for hydrogen atoms as I understand > it, since their behaviour as quantum particles deviate more from a > classical treatment than is the case for heavier nuclei. This is > mentioned in the gromacs manual. > > /Erik This depends on the system you study. In some cases it is necessary not to constrain the hydrogen atoms to get a better agreement with the experiment. Also, if one needs to deal with vibrational spectra involving hydrogens, they must be mobile. Ran. Date: Wed, 11 Nov 2009 21:45:44 +0100 From: Tsjerk Wassenaar Subject: Re: [gmx-users] Constraints & Restraints To: Discussion list for GROMACS users Message-ID: <8ff89815091245u63c6aa65sa839f24634352...@mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Darrell, Constraints and restraints also apply to relative positions. A bond constraint fixes the bond to a certain distance. constraints = all-bonds means that all bonds are to be converted to constraints, rather than have them flexible, e.g. harmonic. Harmonic bonds are actually more like restraints, penalizing deviations from the equilibrium values. These equilibrium values and the 'penalty function' are described in the force field. Hope it helps, Tsjerk On Wed, Nov 11, 2009 at 9:32 PM, wrote: > Hi, > I just have a quick question on contraints and restraints. My > understanding is that "constraints" fix the position of an atom in > space and "restraints" restrain the deviation of the atom's position > from its equilibrium point. Is that correct? If so, then I am a > little > confused by the purpose of "constraints = all-bonds" or "constraints > = none" in an mdp file, since by selection of a force field, which > has > bond/angle/dihedral stretching/bending/torsion constants, we are > specifying the constraints applied to the simulation. So then what is > the purpose of "constraints = all-bonds" and "constraints = none"? > > Thanks. > > Darrell > > > -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman -- -- 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] Constraints & Restraints
Darrell Koskinen wrote: Thanks for the additional comments. So given that, in my system, I have H atoms attached to C atoms on the perimeter of a finite graphene sheet that is placed above multiple infinite layers of graphene (graphite), would it be more appropriate to use: (i) a classical (harmonic) model using constraints=none or (ii) a constrained model using constraints=all-bonds? Is there a precedent established in the literature? Spectroscopic data that can justify your choice? Constraints are generally reasonable for bonds that are in the ground state, so your choice will also be motivated by the conditions you're trying to simulate. Note that, currently, I use constraints=none and see that the C atoms in the graphene sheet are well behaved and not vibrating very much, but the H atoms on the perimeter are vibrating wildly. Would you have any idea of whether this is natural and to be expected or not? Maybe this is an indication that constraints should be used in this particular model. However, I have no idea whether it is natural for hydrogen atoms to flip and flop around so much on the edge of a graphene sheet. I guess it depends on what you mean by "wildly." It could just be that you're using too large of a time step, generating an unstable trajectory. In the absence of constraints, you cannot necessarily guarantee stable integration with dt greater than 1 fs. Again, spectroscopic information (if available) would probably give you an indication on the vibrational frequencies of bonds involving hydrogen atoms. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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] Adsorption energy of a single molecule
Hi Mark,
No, I am not trying to build a random number generator and hope that I
am not moving in this direction : )
My definition of adsorption energy would be the difference in energy
when two species are at an infinite distance and the energy when these
species are at an equilibrium distance from each other.
I think the way in which I can measure this energy difference would be
to subtract the LJ (LR) energy between an ammonia molecule and the
graphene sheet (where the distance between the molecule and the graphene
sheet is large) from the LJ (SR) energy between an adsorbed ammonia
molecule and the graphene sheet.
I am not aware that OPLS-AA was parameterized to produce such values,
but would appreciate your comments.
Thanks.
Darrell
Message: 2
Date: Thu, 12 Nov 2009 10:42:24 +1100
From: Mark Abraham
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4afb4be0.1020...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Darrell Koskinen wrote:
Hi Justin,
So when I create the index file with the molecule and the graphene sheet
and run g_energy, is the adsorption energy between the adsorbed molecule
and the graphene sheet the LJ (SR) energy?
Not necessarily, unless the force field was parameterized to produce
such values. First, seek to define what you mean by adsorption (free)
energy, then consider how a simulation might measure that. Then,
consider whether any force fields exist that might achieve that. Then,
test it on a case where you have experimental data.
Other procedures run a much higher risk of producing an expensive random
number generator :-)
And will this energy be just
the interaction energy between the adsorbed molecule and the graphene
sheet (i.e. does the creation of the new index file and executing -rerun
cause g_energy to exclude the energies between the other molecules and
the graphene sheet)?
Creating an energy group causes mdrun -rerun to report the fraction of
the total nonbonded energies that are due to intra- and inter-group
interactions. See manual section 3.3
Mark
Date: Sun, 01 Nov 2009 21:27:19 -0500
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4aee4387.40...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Darrell Koskinen wrote:
Hi Justin,
Since I cannot use the original .tpr file, then do I need to run
grompp with the new index file to create a "new" .tpr file,
"mdtopolnew.tpr"? I assume I then need to modify the energygrps line
within the .mdp file to include these new energy groups and then
execute "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr". Is this correct?
Yes, that is the point of the -rerun function.
Does executing "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr" cause a
molecular dynamics simulation to run once again? If so, then will the
exact same molecules that adsorbed on the first MD run be the same
ones that adsorb on the second MD run?
The original coordinates are used to re-calculate the energies. No
new simulation is performed.
-Justin
Thanks.
Darrell
***
***
Date: Sun, 01 Nov 2009 19:29:36 -0500
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Adsorption energy of a single molecule
To: Discussion list for GROMACS users
Message-ID: <4aee27f0.50...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Darrell Koskinen wrote:
Hi Justin,
In my simulation, I have just over 100 ammonia molecules and, of
these > molecules, 10 to 20 adsorb onto the graphene sheet. I
initially thought > that I would need to tag each one of the ammonia
molecules, since I > would not know, in advance of running the
simulation, which of these > molecules would adsorb.
Are you suggesting that, after the initial simulation run, which
uses an > index file "index.ndx" and is comprised of three
components {System, > Grph, NH3}, I run make_ndx again to assign
each adsorbed molecule to its > own index, execute "mdrun -rerun
mdtraj.trr -s mdtopol.tpr", where > mdtraj.trr and mdtopol.tpr are
the output of the initial simulation, and > then use g_energy to
analyze the energies between the groups?
Almost. You can't use the original .tpr file if you are trying to
establish new energy monitoring groups. Hence the point of making a
new .mdp file. So, re-run the old trajectory with the new .tpr file
to take advantage of the new groups.
-Justin
-- Justin A. Lemkul Ph.D.
Candidate ICTAS Doctoral Scholar Department of Biochemistry Virgi
Re: [gmx-users] Adsorption energy of a single molecule
Darrell Koskinen wrote: Hi Mark, No, I am not trying to build a random number generator and hope that I am not moving in this direction : ) My definition of adsorption energy would be the difference in energy when two species are at an infinite distance and the energy when these species are at an equilibrium distance from each other. OK, but I think you need to measure a free energy change, using (for example) a PMF generated by the pulling code in GROMACS. I think the way in which I can measure this energy difference would be to subtract the LJ (LR) energy between an ammonia molecule and the graphene sheet (where the distance between the molecule and the graphene sheet is large) from the LJ (SR) energy between an adsorbed ammonia molecule and the graphene sheet. That assumes an unrealistic independence of the forcefield contributions. Why would energy not partition over bonded and Coulombic interactions also? Also, the distinction between LR and SR is merely to do with your twin-range cut-off choices (read manual!). The adsorption process is a transition from no interaction (i.e. outside the LR cutoff) to physical contact. The total LJ interaction energy (if that means anything!) will be partitioned between LR and SR according to distance from the surface. I am not aware that OPLS-AA was parameterized to produce such values, but would appreciate your comments. I know nothing about OPLS-AA, but would guess that it wasn't parameterized for graphite, gaseous ammonia or to reproduce adsorption energies. I think you'd have to demonstrate (through simulation or literature reference) suitable behaviour of graphite and gaseous ammonia on their own before trying to simulate them together. If there's some kind of experimental observable about the behaviour of adsorbed ammonia on graphite that you could reproduce, that would be a useful indicator that the force field is doing OK. Absent that, you might just have that random number generator :-) Mark Message: 2 Date: Thu, 12 Nov 2009 10:42:24 +1100 From: Mark Abraham Subject: Re: [gmx-users] Adsorption energy of a single molecule To: Discussion list for GROMACS users Message-ID: <4afb4be0.1020...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi Justin, So when I create the index file with the molecule and the graphene sheet and run g_energy, is the adsorption energy between the adsorbed molecule and the graphene sheet the LJ (SR) energy? Not necessarily, unless the force field was parameterized to produce such values. First, seek to define what you mean by adsorption (free) energy, then consider how a simulation might measure that. Then, consider whether any force fields exist that might achieve that. Then, test it on a case where you have experimental data. Other procedures run a much higher risk of producing an expensive random number generator :-) And will this energy be just the interaction energy between the adsorbed molecule and the graphene sheet (i.e. does the creation of the new index file and executing -rerun cause g_energy to exclude the energies between the other molecules and the graphene sheet)? Creating an energy group causes mdrun -rerun to report the fraction of the total nonbonded energies that are due to intra- and inter-group interactions. See manual section 3.3 Mark Date: Sun, 01 Nov 2009 21:27:19 -0500 From: "Justin A. Lemkul" Subject: Re: [gmx-users] Adsorption energy of a single molecule To: Discussion list for GROMACS users Message-ID: <4aee4387.40...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi Justin, Since I cannot use the original .tpr file, then do I need to run grompp with the new index file to create a "new" .tpr file, "mdtopolnew.tpr"? I assume I then need to modify the energygrps line within the .mdp file to include these new energy groups and then execute "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr". Is this correct? Yes, that is the point of the -rerun function. Does executing "mdrun -rerun mdtraj.trr -s mdtopolnew.tpr" cause a molecular dynamics simulation to run once again? If so, then will the exact same molecules that adsorbed on the first MD run be the same ones that adsorb on the second MD run? The original coordinates are used to re-calculate the energies. No new simulation is performed. -Justin Thanks. Darrell *** *** Date: Sun, 01 Nov 2009 19:29:36 -0500 From: "Justin A. Lemkul" Subject: Re: [gmx-users] Adsorption energy of a single molecule To: Discussion list for GROMACS users Message-ID: <4aee27f0.50...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi Justi
Re: [gmx-users] Density histogram in Ramachandran plot
ms wrote: Hi, I wonder if there is an easy way I am missing to get a density histogram from the Ramachandran plot over a trajectory as outputted by g_rama. All I see are big, uniform black blobs and they're not helpful, because with tons of data points a density plot would be much more informative. Thanks! It's not quite what you want, but using -dt you can have fewer data points. Bear in mind that trajectory snapshots "too close" in time aren't independent data anyway... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Generate an Index File
I am trying to run g_dist c:\ProgramData\BOINC\slots\0>g_dist.exe -f md.xtc -s md.tpr --- Program g_dist, VERSION 4.0.5 Source code file: futil.c, line: 330 File input/output error: index.ndx --- Thanx for Using GROMACS - Have a Nice Day so I tried mdrun with the -dn option mdrun.exe -dn -v -x -deffnm md It failed to generate an index file. What am I doing wrong? -- Jack http://drugdiscoveryathome.com http://hydrogenathome.org -- 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] Generate an Index File
Jack Shultz wrote: I am trying to run g_dist c:\ProgramData\BOINC\slots\0>g_dist.exe -f md.xtc -s md.tpr --- Program g_dist, VERSION 4.0.5 Source code file: futil.c, line: 330 File input/output error: index.ndx --- Thanx for Using GROMACS - Have a Nice Day so I tried mdrun with the -dn option mdrun.exe -dn -v -x -deffnm md It failed to generate an index file. What am I doing wrong? See http://www.gromacs.org/index.php?title=Documentation/File_Formats/Index_File Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Generate an Index File
Jack Shultz wrote: I am trying to run g_dist c:\ProgramData\BOINC\slots\0>g_dist.exe -f md.xtc -s md.tpr --- Program g_dist, VERSION 4.0.5 Source code file: futil.c, line: 330 File input/output error: index.ndx --- Thanx for Using GROMACS - Have a Nice Day so I tried mdrun with the -dn option mdrun.exe -dn -v -x -deffnm md It failed to generate an index file. What am I doing wrong? You're using the wrong tool; make_ndx is used to make index groups (hence the name). The -dn option of mdrun is some special function, apparently related to dipoles. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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
