Re: [gmx-users] PROTEIN FOLDING
Hi, Thank you for your prompt reply. By clustering analysis, are you talking about gmx cluster command? "over particular PC sub space" Could you please elaborate a bit? Thanks a lot once again. Thanks, Neha On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH wrote: > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta > wrote: > > > Hi gromacs users, > > > > After MD simulation of protein-ligand complex for 5ns, can we view > protein > > folding? > > > > How to do it? > > > > I want to ascertain if there is any conformation change in protein where > > the ligand binds. Is it possible? > > > > We observe hydrogen bonds through molecular docking. Hence, I want to > make > > observation through MD simulation which is not obtained through docking. > > > You can perform Clustering analysis over particular PC sub space to measure > the structural changes. > > > > > > > Can someone help me regarding this? > > > > Thank you very much in advance. > > > > Thanks, > > Neha > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PROTEIN FOLDING
On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta wrote: > Hi, > > > Thank you for your prompt reply. > > By clustering analysis, are you talking about gmx cluster command? > > "over particular PC sub space" > > Could you please elaborate a bit? Yea clustering analysis can interpret a lot datas about your complex simulation. Note: I am not sure whether you Can perform gmx cluster over particular sub space. > > > Thanks a lot once again. > > Thanks, > Neha > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH > wrote: > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta > > wrote: > > > > > Hi gromacs users, > > > > > > After MD simulation of protein-ligand complex for 5ns, can we view > > protein > > > folding? > > > > > > How to do it? > > > > > > I want to ascertain if there is any conformation change in protein > where > > > the ligand binds. Is it possible? > > > > > > We observe hydrogen bonds through molecular docking. Hence, I want to > > make > > > observation through MD simulation which is not obtained through > docking. > > > > > > You can perform Clustering analysis over particular PC sub space to > measure > > the structural changes. > > > > > > > > > > > Can someone help me regarding this? > > > > > > Thank you very much in advance. > > > > > > Thanks, > > > Neha > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > *Regards,* > > *Rahul Suresh* > > *Research Scholar* > > *Bharathiar University* > > *Coimbatore* > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PROTEIN FOLDING
Also you must know, a lot analysis are available over the entire manual of Gromacs where all cannot be performed. Gromacs always provide you all necessary analysis but to choose which one is always your choice that suits your simulation purpose. On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta wrote: > Hi, > > > Thank you for your prompt reply. > > By clustering analysis, are you talking about gmx cluster command? > > "over particular PC sub space" > > Could you please elaborate a bit? > > Thanks a lot once again. > > Thanks, > Neha > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH > wrote: > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta > > wrote: > > > > > Hi gromacs users, > > > > > > After MD simulation of protein-ligand complex for 5ns, can we view > > protein > > > folding? > > > > > > How to do it? > > > > > > I want to ascertain if there is any conformation change in protein > where > > > the ligand binds. Is it possible? > > > > > > We observe hydrogen bonds through molecular docking. Hence, I want to > > make > > > observation through MD simulation which is not obtained through > docking. > > > > > > You can perform Clustering analysis over particular PC sub space to > measure > > the structural changes. > > > > > > > > > > > Can someone help me regarding this? > > > > > > Thank you very much in advance. > > > > > > Thanks, > > > Neha > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > *Regards,* > > *Rahul Suresh* > > *Research Scholar* > > *Bharathiar University* > > *Coimbatore* > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Measuring distance to the nearest image
Hi Anthony, I assume you've seen the -pbc flag of gmx distance; and IIRC there's also some options for that in the selection syntax. I'm not sure that'll do what you want though. If you're going to make a script, have a look at the Python module MDAnalysis, that has some nifty tools. If you strictly use cubic boxes you can take the modulus of the distance you measured --- but that'll bite you at some point in the future. Peter On 19-12-17 07:06, Anthony Nash wrote: > > Just wondering whether anyone has had any luck with a similar problem? If > not, I’ll knock a script together and make it available. I was hoping not to > reinvent the wheel if there was already a way. > > Regards > Anthony > > On 18/12/2017 06:23, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on > behalf of Anthony Nash" behalf of anthony.n...@dpag.ox.ac.uk> wrote: > > > Hi all, > > I am trying to measure the distance between the COM of two side chain > functional groups across the periodic boundary to their nearest image rather > than across the unit cell itself. I have tried several gromacs distance > commands with no success and more at random as I trawl through the help and > manual, so I won’t replicate those commands here. > > This link is a hand drawn image of what I am trying to do. I would like > to measure how far apart the two large dots are across the periodic boundary. > VMD gives me roughly 1 nm, but the Gromacs commands give me 8 nm as it takes > the measurement from within the unit cell. > > > https://www.researchgate.net/profile/Anthony_Nash3/post/How_to_calculate_distance_between_groups_into_the_nearest_image_using_Gromacs/attachment/5a30d10eb53d2f0bba43e5c3/AS:571001131417600@1513148686095/image/IMG_20171213_065534.jpg > If this involve a tcl script in VMD I would appreciate knowing how to > code for an atom selection in a “Periodic” image rather than the “Self”. > > Loads of thanks! > Anthony > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PROTEIN FOLDING
Ok..Thank you.. I'll extend my simulation upto 50 ns. Thanks, Neha On Tue, Dec 19, 2017 at 12:44 PM, Nikhil Maroli wrote: > After MD simulation of protein-ligand complex for 5ns, can we view protein > folding? > > mostly, NO > > Search what time range 'protein folding' is happening. > > How to do it? > > I want to ascertain if there is any conformation change in protein where > the ligand binds. Is it possible? > > > You might want to do PCA, RMSD and DSSP > > We observe hydrogen bonds through molecular docking. Hence, I want to make > observation through MD simulation which is not obtained through docking. > > > gmx hbond > > Can someone help me regarding this? > > > i really wondering what is possible in 5 ns simulation time, you may > try to extend it up to 100 ns or atleast a 50 ns. > > Thank you very much in advance. > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Measuring distance to the nearest image
Hi Anthony, Would it work if you take x/y/z components of the distance and subtract ones extending the size of the box in the corresponding direction? You will need to extract box size from the *.edr file (unless box is of fixed size), further use flag -oxyz from gmx distance for xyz distance components. -Alexandr On 19/12/2017 11:05, Peter Kroon wrote: Hi Anthony, I assume you've seen the -pbc flag of gmx distance; and IIRC there's also some options for that in the selection syntax. I'm not sure that'll do what you want though. If you're going to make a script, have a look at the Python module MDAnalysis, that has some nifty tools. If you strictly use cubic boxes you can take the modulus of the distance you measured --- but that'll bite you at some point in the future. Peter On 19-12-17 07:06, Anthony Nash wrote: Just wondering whether anyone has had any luck with a similar problem? If not, I’ll knock a script together and make it available. I was hoping not to reinvent the wheel if there was already a way. Regards Anthony On 18/12/2017 06:23, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Anthony Nash" wrote: Hi all, I am trying to measure the distance between the COM of two side chain functional groups across the periodic boundary to their nearest image rather than across the unit cell itself. I have tried several gromacs distance commands with no success and more at random as I trawl through the help and manual, so I won’t replicate those commands here. This link is a hand drawn image of what I am trying to do. I would like to measure how far apart the two large dots are across the periodic boundary. VMD gives me roughly 1 nm, but the Gromacs commands give me 8 nm as it takes the measurement from within the unit cell. https://www.researchgate.net/profile/Anthony_Nash3/post/How_to_calculate_distance_between_groups_into_the_nearest_image_using_Gromacs/attachment/5a30d10eb53d2f0bba43e5c3/AS:571001131417600@1513148686095/image/IMG_20171213_065534.jpg If this involve a tcl script in VMD I would appreciate knowing how to code for an atom selection in a “Periodic” image rather than the “Self”. Loads of thanks! Anthony -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Measuring distance to the nearest image
Hi This is exactly what two well chosen selections should produce, given a tpr and the PBC option. What have you tried that didn't work as you expected? Mark On Mon, Dec 18, 2017, 5:23 PM Anthony Nash wrote: > > Hi all, > > I am trying to measure the distance between the COM of two side chain > functional groups across the periodic boundary to their nearest image > rather than across the unit cell itself. I have tried several gromacs > distance commands with no success and more at random as I trawl through the > help and manual, so I won’t replicate those commands here. > > This link is a hand drawn image of what I am trying to do. I would like to > measure how far apart the two large dots are across the periodic boundary. > VMD gives me roughly 1 nm, but the Gromacs commands give me 8 nm as it > takes the measurement from within the unit cell. > > > https://www.researchgate.net/profile/Anthony_Nash3/post/How_to_calculate_distance_between_groups_into_the_nearest_image_using_Gromacs/attachment/5a30d10eb53d2f0bba43e5c3/AS:571001131417600@1513148686095/image/IMG_20171213_065534.jpg > If this involve a tcl script in VMD I would appreciate knowing how to code > for an atom selection in a “Periodic” image rather than the “Self”. > > Loads of thanks! > Anthony > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Measuring distance to the nearest image
Hi Alexandr, Those were my thoughts also. I was just hoping there was something out there already written to save me time. Thanks Anthony Dr Anthony Nash BSc (Hons) MSc MSc PhD MRSC Department of Physiology, Anatomy & Genetics Oxford University OX1 3PT UK On 19/12/2017 10:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Alexandr Nasedkin" wrote: Hi Anthony, Would it work if you take x/y/z components of the distance and subtract ones extending the size of the box in the corresponding direction? You will need to extract box size from the *.edr file (unless box is of fixed size), further use flag -oxyz from gmx distance for xyz distance components. -Alexandr On 19/12/2017 11:05, Peter Kroon wrote: > Hi Anthony, > > > I assume you've seen the -pbc flag of gmx distance; and IIRC there's > also some options for that in the selection syntax. I'm not sure that'll > do what you want though. > > If you're going to make a script, have a look at the Python module > MDAnalysis, that has some nifty tools. > > If you strictly use cubic boxes you can take the modulus of the distance > you measured --- but that'll bite you at some point in the future. > > > Peter > > > On 19-12-17 07:06, Anthony Nash wrote: >> Just wondering whether anyone has had any luck with a similar problem? If not, I’ll knock a script together and make it available. I was hoping not to reinvent the wheel if there was already a way. >> >> Regards >> Anthony >> >> On 18/12/2017 06:23, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Anthony Nash" wrote: >> >> >> Hi all, >> >> I am trying to measure the distance between the COM of two side chain functional groups across the periodic boundary to their nearest image rather than across the unit cell itself. I have tried several gromacs distance commands with no success and more at random as I trawl through the help and manual, so I won’t replicate those commands here. >> >> This link is a hand drawn image of what I am trying to do. I would like to measure how far apart the two large dots are across the periodic boundary. VMD gives me roughly 1 nm, but the Gromacs commands give me 8 nm as it takes the measurement from within the unit cell. >> >> https://www.researchgate.net/profile/Anthony_Nash3/post/How_to_calculate_distance_between_groups_into_the_nearest_image_using_Gromacs/attachment/5a30d10eb53d2f0bba43e5c3/AS:571001131417600@1513148686095/image/IMG_20171213_065534.jpg >> If this involve a tcl script in VMD I would appreciate knowing how to code for an atom selection in a “Periodic” image rather than the “Self”. >> >> Loads of thanks! >> Anthony >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. >> > > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Measuring distance to the nearest image
Hi Mark, As an example, from numerous attempts, I have tried: /usr/local/gromacs5.1.2/bin/gmx_d distance -pbc -b 1 -f crosslinked_0_20.trr -s crosslinked_0_20.tpr -n index.ndx which was throwing a value of around 8 nm, rather than the 2 nm I was expecting if it took a measurement from over the periodic boundary. Unfortunately, I’ve left the necessary harddrive at home. I’’’ be more than happy to respond with a more comprehensive example along with output data in a few hours. Thanks Anthony On 19/12/2017 11:02, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham" wrote: Hi This is exactly what two well chosen selections should produce, given a tpr and the PBC option. What have you tried that didn't work as you expected? Mark On Mon, Dec 18, 2017, 5:23 PM Anthony Nash wrote: > > Hi all, > > I am trying to measure the distance between the COM of two side chain > functional groups across the periodic boundary to their nearest image > rather than across the unit cell itself. I have tried several gromacs > distance commands with no success and more at random as I trawl through the > help and manual, so I won’t replicate those commands here. > > This link is a hand drawn image of what I am trying to do. I would like to > measure how far apart the two large dots are across the periodic boundary. > VMD gives me roughly 1 nm, but the Gromacs commands give me 8 nm as it > takes the measurement from within the unit cell. > > > https://www.researchgate.net/profile/Anthony_Nash3/post/How_to_calculate_distance_between_groups_into_the_nearest_image_using_Gromacs/attachment/5a30d10eb53d2f0bba43e5c3/AS:571001131417600@1513148686095/image/IMG_20171213_065534.jpg > If this involve a tcl script in VMD I would appreciate knowing how to code > for an atom selection in a “Periodic” image rather than the “Self”. > > Loads of thanks! > Anthony > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Measuring distance to the nearest image
Hi, An example where the structure comes from a single frame would be a useful thing to explore whether the code is working correctly. I don't think the composition of the index groups should matter, but I can't see how the code wouldn't work correctly. Mark On Tue, Dec 19, 2017, 10:12 PM Anthony Nash wrote: > Hi Mark, > > As an example, from numerous attempts, I have tried: > > /usr/local/gromacs5.1.2/bin/gmx_d distance -pbc -b 1 -f > crosslinked_0_20.trr -s crosslinked_0_20.tpr -n index.ndx > > which was throwing a value of around 8 nm, rather than the 2 nm I was > expecting if it took a measurement from over the periodic boundary. > > Unfortunately, I’ve left the necessary harddrive at home. I’’’ be more > than happy to respond with a more comprehensive example along with output > data in a few hours. > > Thanks > Anthony > > > On 19/12/2017 11:02, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Mark Abraham" < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of > mark.j.abra...@gmail.com> wrote: > > Hi > > This is exactly what two well chosen selections should produce, given > a tpr > and the PBC option. What have you tried that didn't work as you > expected? > > Mark > > On Mon, Dec 18, 2017, 5:23 PM Anthony Nash > > wrote: > > > > > Hi all, > > > > I am trying to measure the distance between the COM of two side chain > > functional groups across the periodic boundary to their nearest image > > rather than across the unit cell itself. I have tried several gromacs > > distance commands with no success and more at random as I trawl > through the > > help and manual, so I won’t replicate those commands here. > > > > This link is a hand drawn image of what I am trying to do. I would > like to > > measure how far apart the two large dots are across the periodic > boundary. > > VMD gives me roughly 1 nm, but the Gromacs commands give me 8 nm as > it > > takes the measurement from within the unit cell. > > > > > > > https://www.researchgate.net/profile/Anthony_Nash3/post/How_to_calculate_distance_between_groups_into_the_nearest_image_using_Gromacs/attachment/5a30d10eb53d2f0bba43e5c3/AS:571001131417600@1513148686095/image/IMG_20171213_065534.jpg > > If this involve a tcl script in VMD I would appreciate knowing how > to code > > for an atom selection in a “Periodic” image rather than the “Self”. > > > > Loads of thanks! > > Anthony > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Umbrella sampling
Hi all I am doing umbrella sampling taking distance between COM as a reaction coordinate. when I am trying to calculate PMF using the following command gmx wham -it tpr-files.dat -if pullf-files.dat -o free.xvg -hist hist.xvg I got an error Program: gmx wham, version 2016.3 Source file: src/gromacs/gmxana/gmx_wham.cpp (line 1821) Fatal error: Unknown file type of . Should be tpr, xvg, or pdo. my tpr-files.dat is umbrella0.tpr umbrella1.tpr umbrella2.tpr umbrella3.tpr umbrella4.tpr umbrella5.tpr umbrella6.tpr umbrella7.tpr umbrella8.tpr umbrella9.tpr umbrella10.tpr umbrella11.tpr umbrella12.tpr and pullf-files.dat is pullf0.xvg pullf1.xvg pullf2.xvg pullf3.xvg pullf4.xvg pullf5.xvg pullf6.xvg pullf7.xvg pullf8.xvg pullf9.xvg pullf10.xvg pullf11.xvg pullf12.xvg And I am using gromacs-2016.3. Can anyone suggest me something? Thanks Sunipa -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Umbrella sampling
Hi, There could be format problem. You can create your own .dat files by typing it. You have probably copied it from somewhere. I hope it will work then. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Grompp error : Incorrect number of parameters
Dear all
For grompp em.mdp I get an error
ERROR 1 [file THC.itp, line 89]:
Incorrect number of parameters - found 2, expected 4 or 8 for U-B.
My itp file as follows
[ angles ]
1 2 29 579.178 109.588 *{Line 89}*
1 2 3 532.192 112.817
2 3 31 551.424 109.189
>From the manual chapter 5, function of U-B is 5. And it works fine for
function type 2 and 8.
Any thing better could be done?
*PS: The itp file is constructed from parameter file of ffTK.*
Thank you
--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
*India*
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
[gmx-users] computing electric field for triclinic system
Dear all, I have system in triclinic box. I'd like to plot a potential map on XY axes for a given Z in triclinic box, i.e. For a fixed value of Z I want to have plot of values in this plane. My system is a periodic "planar" molecule. Scripts using variations of the Ewald summation are mainly intended for orthogonal boxes. I concluded that only script which exists for my purpose is the one used internally by Gromacs. I know that Gromacs converts any triclinic box to a rectangular one. To ensure periodicity Gromacs uses shifted images of the unit cell along the triclinic axis. I'd like to understand how the PME algorithm of Gromacs manages with this issue and if anyone has been doing that. Sincerely, Mariia -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Umbrella sampling
- Message from Dhaniram Mahato - Date: Tue, 19 Dec 2017 21:30:05 +0800 From: Dhaniram Mahato Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling To: gmx-us...@gromacs.org Hi, There could be format problem. You can create your own .dat files by typing it. You have probably copied it from somewhere. I hope it will work then. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Hii Thanks for replying. I have prepared it by own.I have not copied it. - End message from Dhaniram Mahato - -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] computing electric field for triclinic system
which command line is used for SASA? i am using version 5.1.2 On Tue, Dec 19, 2017 at 9:53 PM, Mariia Savenko wrote: > Dear all, > I have system in triclinic box. I'd like to plot a potential map on XY axes > for a given Z in triclinic box, i.e. For a fixed value of Z I want to have > plot of values in this plane. > My system is a periodic "planar" molecule. Scripts using variations of the > Ewald summation are mainly intended for orthogonal boxes. I concluded that > only script which exists for my purpose is the one used internally by > Gromacs. I know that Gromacs converts any triclinic box to a rectangular > one. To ensure periodicity Gromacs uses shifted images of the unit cell > along the triclinic axis. I'd like to understand how the PME algorithm of > Gromacs manages with this issue and if anyone has been doing that. > Sincerely, > Mariia > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] computing electric field for triclinic system
>>* I have a small problem with Gromacs, mainly with doing radius of gyration *>>* calculations, it is all ok with doing the calcualtion, and the command is *>>* fine but my problem is with the units in which the calculation is *>>* performed. It is in picoseconds(ps) but i would like to have it in *>>* nanoseconds(ns) as it is in many publications. If someone could help me *>>* with this problem how to change the units or how to modify the command to *>>* have nanoseconds I would appreciate it. Thanks for all the help* On Tue, Dec 19, 2017 at 10:48 PM, Fakhar Alam wrote: > which command line is used for SASA? i am using version 5.1.2 > > On Tue, Dec 19, 2017 at 9:53 PM, Mariia Savenko > wrote: > >> Dear all, >> I have system in triclinic box. I'd like to plot a potential map on XY >> axes >> for a given Z in triclinic box, i.e. For a fixed value of Z I want to have >> plot of values in this plane. >> My system is a periodic "planar" molecule. Scripts using variations of the >> Ewald summation are mainly intended for orthogonal boxes. I concluded that >> only script which exists for my purpose is the one used internally by >> Gromacs. I know that Gromacs converts any triclinic box to a rectangular >> one. To ensure periodicity Gromacs uses shifted images of the unit cell >> along the triclinic axis. I'd like to understand how the PME algorithm of >> Gromacs manages with this issue and if anyone has been doing that. >> Sincerely, >> Mariia >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support >> /Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Umbrella sampling
- Message from Dhaniram Mahato - Date: Tue, 19 Dec 2017 21:30:05 +0800 From: Dhaniram Mahato Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling To: gmx-us...@gromacs.org Hi, There could be format problem. You can create your own .dat files by typing it. You have probably copied it from somewhere. I hope it will work then. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Hii I have solved the problem. It was just because of one extra space added in the tpr-files.dat file. Now its running properly. - End message from Dhaniram Mahato - -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Gromacs 2018 beta: g_membed broken?
Hello,
Im using g_membed to insert potassium channels into POPC membranes. My
"standard protocol" which worked very well for me on all proteins I used
so far seems to not work with gromacs 2018 (using the exact same input
files).
This is what I am doing:
1) orienting the protein onto the membrane (lambada)
2) Merging the topology files for the membrane and protein
3) grompp: gmx grompp -f g_membed.mdp -n -c input.gro -r input.gro -o
g_membed.tpr --maxwarn 2
4) gmx mdrun -deffnm g_membed -membed embed.dat -mn index.ndx -mp
embedded.top -c embedded.top # selecting protein and membrane group
First thing I noticed is that the number of warnings i have to ignore
during grompp increased by one because of the new PME warning for
charged systems. My protein has a net charge, so I have to choose if i
insert counter ions before or after protein insertion (and I chose to do
it after insertion).
So the warnings I get are:
WARNING 1: You are using Ewald electrostatics in a system with net
charge // I think I can ignore this since I neutralize right after
insertion.
WARNING 2: Can not exclude the lattice Coulomb energy between energy
groups // g_membed does not support verlet
Finally when I run the insertion simulation on the 2018 beta I get the
following error:
step 0: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#
Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#
Wrote pdb files with previous and current coordinates
step 0Warning: Only triclinic boxes with the first vector parallel to
the x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ -nan, -nan, -nan}
Box[ 1]={ -nan, -nan, -nan}
Box[ 2]={ -nan, -nan, -nan}
Can not fix pbc.
This seems to happen independent of my system (I tried several of my
membrane patches and proteins that worked previously). All of them
insert into the membrane with 2016 successfully but fail on the 2018
version. So far I tried to increase the number of steps, reduced the
timestep and played arround with xyinit and zinit as well as setting
-DFLEXIBLE in the mdp, but no success.
Any idea whats wrong? Or should I move this issue directly to redmine
since its related to a version update?
This is my embed.dat file:
nxy = 1000
xyinit = 0.1
xyend = 1.0
rad = 0.22
ndiff = 0
asymmetry = no
pieces = 1
maxwarn = 1
And my mdp:
; Run parameters
integrator = md
nsteps = 1000
dt = 0.002
; I have posres for the protein enabled, although this is irrelevant
because the protein group coords are frozen. Same issue if i disable
this and remove posres!
refcoord_scaling = all
;define = -DFLEXIBLE ; does not help
; membed options
energygrps = insertion_group
freezegrps = insertion_group
freezedim = Y Y Y
energygrp_excl = insertion_group insertion_group
; OUTPUT CONTROL OPTIONS
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 1000
; Bond parameters
continuation = no
constraint_algorithm = lincs
lincs_iter = 2
lincs_order = 8
; CHARMM36 params
constraints = h-bonds
cutoff-scheme = Group ; Verlet is not supported by g_membed
vdwtype = Cut-off
vdw-modifier = force-switch
rlist = 1.2
rvdw = 1.2
rvdw-switch = 0.8
coulombtype = PME
rcoulomb = 1.2
DispCorr = no
; Temperature coupling
tcoupl = V-rescale
tc-grps = Other Water_and_ions Protein
tau_t = 0.1 0.1 0.1
ref-t = 298.0 298.0 298.0
; Pressure coupling
pcoupl = Berendsen
pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
; Periodic boundary conditions
pbc = xyz
; Velocity generation
gen_vel = yes
gen_temp = 298.0
gen_seed = -1
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
comm-mode = Linear
comm-grps = Other Water_and_ions Protein
Best regards,
Daniel
--
Daniel Bauer, M.Sc.
TU Darmstadt
Computational Biology & Simulation
Schnittspahnstr. 2
64287 Darmstadt
ba...@cbs.tu-darmstadt.de
Don't trust atoms, they make up everything.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Umbrella sampling
Out of curiosity, how did you manage to identify and subsequently remove the extra space? I have been having similar problems and the tools I've used haven't fixed this problem. Thanks, From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of sp...@iacs.res.in [sp...@iacs.res.in] Sent: Tuesday, December 19, 2017 6:21 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Umbrella sampling - Message from Dhaniram Mahato - Date: Tue, 19 Dec 2017 21:30:05 +0800 From: Dhaniram Mahato Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling To: gmx-us...@gromacs.org > Hi, > > There could be format problem. You can create your own .dat files by > typing > it. You have probably copied it from somewhere. I hope it will work then. > > https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html > > Thanks > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests > visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or send a mail to gmx-users-requ...@gromacs.org. Hii I have solved the problem. It was just because of one extra space added in the tpr-files.dat file. Now its running properly. - End message from Dhaniram Mahato - -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Semipermeable membrane and pull code/flat bottom restraints for large molecules.
Dear GMX'ers, I'm wondering if you can give me some advice on setting up a system containing a semipermeable membrane. I have seen a few comments on this before, but I think my system is unique enough to warrant a new post. I desire to run a system containing water, and many, largely anisotropic molecules (think rigid hexagons). I wish to slowly squeeze the hexagonal particles within a set region of space, and calculate the force required to contain them (i.e. the osmotic/swelling pressure) as function of semipermeable membrane separation. My current understanding is that this could be achieved several ways: Firstly, I could use flat-bottomed restraints to limit the z space accessible to all hexagonal molecules for a set period of time. I would then need to adjust the flat-bottomed restraints to decrease the semipermeable membrane separation, and continue/iterate the simulation. Alternatively, I could attempt to use the pull code to 'pull' all these molecules together. Again, using flat bottomed restraints in z. I would prefer this method, as I could temporally alter the flat-bottomed restraints within one continuous simulation. My issue with the pull code is that it works on the COM of molecules only. I get the impression that if I use the pull code in gromacs, my molecules may flip, such that a lot of the atoms in the hexagonal molecules are on the wrong side of the semipermeable membrane, whilst the COM of each molecule remains within the flat-bottomed restraints. Is there any way to apply the pull code such that it acts on all atoms within a molecule? I.e. if an atom of my molecule is outside the flat-bottomed restraint, then that atom feels the force from said flat-bottom restraint? Also, I'm assuming that I can work these flat bottom restraints relative to the COM of all of the hexagonal molecules within my system. If I center my system to the COM of all hexagonal molecules prior to commencing my squeeze/simulation, and set comm-grps=HEX (and frequently remove the linear center of mass translation of all hexagonal particles), then my system will remain centered around the said hexagonal molecules as they are squeezed? Apologies for the convoluted and poorly worded questions, but any help on this topic would be appreciated. Will the pull code work for what I am trying to achieve, or am I better off using all-atom flat-bottom restraints (or even some other code/plumed)? All the best, Tom -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Grompp error : Incorrect number of parameters
On 12/19/17 11:14 AM, RAHUL SURESH wrote:
Dear all
For grompp em.mdp I get an error
ERROR 1 [file THC.itp, line 89]:
Incorrect number of parameters - found 2, expected 4 or 8 for U-B.
My itp file as follows
[ angles ]
1 2 29 579.178 109.588 *{Line 89}*
1 2 3 532.192 112.817
2 3 31 551.424 109.189
From the manual chapter 5, function of U-B is 5. And it works fine for
function type 2 and 8.
Any thing better could be done?
As the error tells you, the U-B functional form requires at least 4
parameters; look at its functional form. See Table 5.5.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
[gmx-users] Contact maps using COM distance
I used gmx mdmat in gromacs to create contact maps, but it seems that the mdmat gives the minimum average distance rather than the average centre-of-mass distance. Is there any way to get COM distance in gmx mdmat ? -- Roshan Shrestha M.Sc (Physics) Central Department of Physics, Tribhuvan University Kathmandu, Nepal -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Grompp error : Incorrect number of parameters
Hi,
The CHARMM software implements UB with two separate bond and angle
components, which you probably have to find and to insert here, to suit the
way GROMACS implements the interaction in a self-contained way.
Mark
On Wed, Dec 20, 2017, 10:36 AM Justin Lemkul wrote:
>
>
> On 12/19/17 11:14 AM, RAHUL SURESH wrote:
> > Dear all
> >
> > For grompp em.mdp I get an error
> >
> > ERROR 1 [file THC.itp, line 89]:
> >Incorrect number of parameters - found 2, expected 4 or 8 for U-B.
> >
> > My itp file as follows
> >
> > [ angles ]
> >
> > 1 2 29 579.178 109.588 *{Line 89}*
> > 1 2 3 532.192 112.817
> > 2 3 31 551.424 109.189
> >
> > From the manual chapter 5, function of U-B is 5. And it works fine for
> > function type 2 and 8.
> >
> > Any thing better could be done?
>
> As the error tells you, the U-B functional form requires at least 4
> parameters; look at its functional form. See Table 5.5.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PROTEIN FOLDING
You can try rmsd and gyrate plot to see the changes in your complex. It On Dec 19, 2017 2:22 PM, "RAHUL SURESH" wrote: > Also you must know, a lot analysis are available over the entire manual of > Gromacs where all cannot be performed. Gromacs always provide you all > necessary analysis but to choose which one is always your choice that suits > your simulation purpose. > > > On Tue, 19 Dec 2017 at 1:30 PM, Neha Gupta > wrote: > > > Hi, > > > > > > Thank you for your prompt reply. > > > > By clustering analysis, are you talking about gmx cluster command? > > > > "over particular PC sub space" > > > > Could you please elaborate a bit? > > > > Thanks a lot once again. > > > > Thanks, > > Neha > > > > On Tue, Dec 19, 2017 at 1:22 PM, RAHUL SURESH > > wrote: > > > > > On Tue, 19 Dec 2017 at 12:36 PM, Neha Gupta > > > wrote: > > > > > > > Hi gromacs users, > > > > > > > > After MD simulation of protein-ligand complex for 5ns, can we view > > > protein > > > > folding? > > > > > > > > How to do it? > > > > > > > > I want to ascertain if there is any conformation change in protein > > where > > > > the ligand binds. Is it possible? > > > > > > > > We observe hydrogen bonds through molecular docking. Hence, I want to > > > make > > > > observation through MD simulation which is not obtained through > > docking. > > > > > > > > > You can perform Clustering analysis over particular PC sub space to > > measure > > > the structural changes. > > > > > > > > > > > > > > > Can someone help me regarding this? > > > > > > > > Thank you very much in advance. > > > > > > > > Thanks, > > > > Neha > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > *Regards,* > > > *Rahul Suresh* > > > *Research Scholar* > > > *Bharathiar University* > > > *Coimbatore* > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at http://www.gromacs.org/ > > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Grompp error : Incorrect number of parameters
On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul wrote:
>
>
> On 12/19/17 11:14 AM, RAHUL SURESH wrote:
> > Dear all
> >
> > For grompp em.mdp I get an error
> >
> > ERROR 1 [file THC.itp, line 89]:
> >Incorrect number of parameters - found 2, expected 4 or 8 for U-B.
> >
> > My itp file as follows
> >
> > [ angles ]
> >
> > 1 2 29 579.178 109.588 *{Line 89}*
> > 1 2 3 532.192 112.817
> > 2 3 31 551.424 109.189
> >
> > From the manual chapter 5, function of U-B is 5. And it works fine for
> > function type 2 and 8.
> >
> > Any thing better could be done?
>
> As the error tells you, the U-B functional form requires at least 4
> parameters; look at its functional form. See Table 5.5.
Dear Justin
But the parameter obtained from ffTK have only two. What could be done.?
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Grompp error : Incorrect number of parameters
Hi,
Please read my answer.
Mark
On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH wrote:
> On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul wrote:
>
> >
> >
> > On 12/19/17 11:14 AM, RAHUL SURESH wrote:
> > > Dear all
> > >
> > > For grompp em.mdp I get an error
> > >
> > > ERROR 1 [file THC.itp, line 89]:
> > >Incorrect number of parameters - found 2, expected 4 or 8 for U-B.
> > >
> > > My itp file as follows
> > >
> > > [ angles ]
> > >
> > > 1 2 29 579.178 109.588 *{Line 89}*
> > > 1 2 3 532.192 112.817
> > > 2 3 31 551.424 109.189
> > >
> > > From the manual chapter 5, function of U-B is 5. And it works fine for
> > > function type 2 and 8.
> > >
> > > Any thing better could be done?
> >
> > As the error tells you, the U-B functional form requires at least 4
> > parameters; look at its functional form. See Table 5.5.
>
>
> Dear Justin
>
> But the parameter obtained from ffTK have only two. What could be done.?
>
> >
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalem...@vt.edu | (540) 231-3129
> > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Grompp error : Incorrect number of parameters
Sorry Mark, I failed to note that.
I am afraid that I don't know what that are those components and how and
where to find it. If you are actually meaning about "ub0 kub" components,
how could i find the value for it. In case of swiss param generated itp
file, these components appear to be 0. Any help here please?
On Wed, Dec 20, 2017 at 10:19 AM, Mark Abraham
wrote:
> Hi,
>
> Please read my answer.
>
> Mark
>
> On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH
> wrote:
>
> > On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul wrote:
> >
> > >
> > >
> > > On 12/19/17 11:14 AM, RAHUL SURESH wrote:
> > > > Dear all
> > > >
> > > > For grompp em.mdp I get an error
> > > >
> > > > ERROR 1 [file THC.itp, line 89]:
> > > >Incorrect number of parameters - found 2, expected 4 or 8 for U-B.
> > > >
> > > > My itp file as follows
> > > >
> > > > [ angles ]
> > > >
> > > > 1 2 29 579.178 109.588 *{Line 89}*
> > > > 1 2 3 532.192 112.817
> > > > 2 3 31 551.424 109.189
> > > >
> > > > From the manual chapter 5, function of U-B is 5. And it works fine
> for
> > > > function type 2 and 8.
> > > >
> > > > Any thing better could be done?
> > >
> > > As the error tells you, the U-B functional form requires at least 4
> > > parameters; look at its functional form. See Table 5.5.
> >
> >
> > Dear Justin
> >
> > But the parameter obtained from ffTK have only two. What could be done.?
> >
> > >
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> > > Virginia Tech Department of Biochemistry
> > >
> > > 303 Engel Hall
> > > 340 West Campus Dr.
> > > Blacksburg, VA 24061
> > >
> > > jalem...@vt.edu | (540) 231-3129
> > > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > >
> > > ==
> > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Grompp error : Incorrect number of parameters
Hi,
Sorry I don't know how any of these non-GROMACS tools work, or even whether
they actually generate Urey Bradley interactions that have all the terms. I
suggest you spend some time with the documentation.
Mark
On Wed, Dec 20, 2017, 5:15 PM RAHUL SURESH wrote:
> Sorry Mark, I failed to note that.
>
> I am afraid that I don't know what that are those components and how and
> where to find it. If you are actually meaning about "ub0 kub" components,
> how could i find the value for it. In case of swiss param generated itp
> file, these components appear to be 0. Any help here please?
>
>
> On Wed, Dec 20, 2017 at 10:19 AM, Mark Abraham
> wrote:
>
> > Hi,
> >
> > Please read my answer.
> >
> > Mark
> >
> > On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH
> > wrote:
> >
> > > On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul wrote:
> > >
> > > >
> > > >
> > > > On 12/19/17 11:14 AM, RAHUL SURESH wrote:
> > > > > Dear all
> > > > >
> > > > > For grompp em.mdp I get an error
> > > > >
> > > > > ERROR 1 [file THC.itp, line 89]:
> > > > >Incorrect number of parameters - found 2, expected 4 or 8 for
> U-B.
> > > > >
> > > > > My itp file as follows
> > > > >
> > > > > [ angles ]
> > > > >
> > > > > 1 2 29 579.178 109.588 *{Line 89}*
> > > > > 1 2 3 532.192 112.817
> > > > > 2 3 31 551.424 109.189
> > > > >
> > > > > From the manual chapter 5, function of U-B is 5. And it works fine
> > for
> > > > > function type 2 and 8.
> > > > >
> > > > > Any thing better could be done?
> > > >
> > > > As the error tells you, the U-B functional form requires at least 4
> > > > parameters; look at its functional form. See Table 5.5.
> > >
> > >
> > > Dear Justin
> > >
> > > But the parameter obtained from ffTK have only two. What could be
> done.?
> > >
> > > >
> > > >
> > > > -Justin
> > > >
> > > > --
> > > > ==
> > > >
> > > > Justin A. Lemkul, Ph.D.
> > > > Assistant Professor
> > > > Virginia Tech Department of Biochemistry
> > > >
> > > > 303 Engel Hall
> > > > 340 West Campus Dr.
> > > > Blacksburg, VA 24061
> > > >
> > > > jalem...@vt.edu | (540) 231-3129
> > > > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > > >
> > > > ==
> > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > *Regards,*
> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Grompp error : Incorrect number of parameters
Hi
Thank you Mark.
On Wed, Dec 20, 2017 at 12:29 PM, Mark Abraham
wrote:
> Hi,
>
> Sorry I don't know how any of these non-GROMACS tools work, or even whether
> they actually generate Urey Bradley interactions that have all the terms. I
> suggest you spend some time with the documentation.
>
> Mark
>
> On Wed, Dec 20, 2017, 5:15 PM RAHUL SURESH
> wrote:
>
> > Sorry Mark, I failed to note that.
> >
> > I am afraid that I don't know what that are those components and how and
> > where to find it. If you are actually meaning about "ub0 kub"
> components,
> > how could i find the value for it. In case of swiss param generated itp
> > file, these components appear to be 0. Any help here please?
> >
> >
> > On Wed, Dec 20, 2017 at 10:19 AM, Mark Abraham >
> > wrote:
> >
> > > Hi,
> > >
> > > Please read my answer.
> > >
> > > Mark
> > >
> > > On Wed, Dec 20, 2017, 3:43 PM RAHUL SURESH
> > > wrote:
> > >
> > > > On Wed, 20 Dec 2017 at 5:06 AM, Justin Lemkul
> wrote:
> > > >
> > > > >
> > > > >
> > > > > On 12/19/17 11:14 AM, RAHUL SURESH wrote:
> > > > > > Dear all
> > > > > >
> > > > > > For grompp em.mdp I get an error
> > > > > >
> > > > > > ERROR 1 [file THC.itp, line 89]:
> > > > > >Incorrect number of parameters - found 2, expected 4 or 8 for
> > U-B.
> > > > > >
> > > > > > My itp file as follows
> > > > > >
> > > > > > [ angles ]
> > > > > >
> > > > > > 1 2 29 579.178 109.588 *{Line 89}*
> > > > > > 1 2 3 532.192 112.817
> > > > > > 2 3 31 551.424 109.189
> > > > > >
> > > > > > From the manual chapter 5, function of U-B is 5. And it works
> fine
> > > for
> > > > > > function type 2 and 8.
> > > > > >
> > > > > > Any thing better could be done?
> > > > >
> > > > > As the error tells you, the U-B functional form requires at least 4
> > > > > parameters; look at its functional form. See Table 5.5.
> > > >
> > > >
> > > > Dear Justin
> > > >
> > > > But the parameter obtained from ffTK have only two. What could be
> > done.?
> > > >
> > > > >
> > > > >
> > > > > -Justin
> > > > >
> > > > > --
> > > > > ==
> > > > >
> > > > > Justin A. Lemkul, Ph.D.
> > > > > Assistant Professor
> > > > > Virginia Tech Department of Biochemistry
> > > > >
> > > > > 303 Engel Hall
> > > > > 340 West Campus Dr.
> > > > > Blacksburg, VA 24061
> > > > >
> > > > > jalem...@vt.edu | (540) 231-3129
> > > > > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > > > >
> > > > > ==
> > > > >
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > > --
> > > > *Regards,*
> > > > *Rahul Suresh*
> > > > *Research Scholar*
> > > > *Bharathiar University*
> > > > *Coimbatore*
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
--
*Regards,*
*Rahul Sur
