[gmx-users] carbon nanotube - ifnite in length ?
Dear Gmx Users, I have my carbon nanotube and I wish to make it infinite in lenght. Which mdp options whall be used? pbc = xy and z is the infinite dimension? another issue: Would you apply bonds between carbon atoms within the nanotube or constraints using LINCS? Which of them is less computationally expensive for the run? Thank you in advance, Steven -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] carbon nanotube - ifnite in length ?
I think this is in topology, not in MDP. With PBC, you just specify what happens to the particle after it crosses the edge of the box in certain direction. I have no preference regarding LINCS vs harmonic bonds. You can also "freeze" only the rim atoms of the nanotube from both ends and this will be almost the same as infinite tube. This solution is faster on my taste. Dr. Vitaly V. Chaban On Thu, Sep 26, 2013 at 2:39 PM, Steven Neumann wrote: > Dear Gmx Users, > > I have my carbon nanotube and I wish to make it infinite in lenght. Which > mdp options whall be used? pbc = xy and z is the infinite dimension? > another issue: Would you apply bonds between carbon atoms within the > nanotube or constraints using LINCS? Which of them is less computationally > expensive for the run? > > Thank you in advance, > > Steven > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] trjcat after trjconv
Dear all, I have a basic doubt. Is there any difference between the two processes where 1) I concatenate the trajectories and do trjconv to remove PBC, which is a default process 2) Do trjconv on all the xtc files separately and then concatenate them. Thank you for your time -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat after trjconv
I do not think that I ever tried myself, but is seems all the same. Why do you ask? Dr. Vitaly V. Chaban On Thu, Sep 26, 2013 at 3:40 PM, Venkat Reddy wrote: > Dear all, > I have a basic doubt. Is there any difference between the two processes > where > 1) I concatenate the trajectories and do trjconv to remove PBC, which is a > default process > 2) Do trjconv on all the xtc files separately and then concatenate them. > > Thank you for your time > > -- > With Best Wishes > Venkat Reddy Chirasani > PhD student > Laboratory of Computational Biophysics > Department of Biotechnology > IIT Madras > Chennai > INDIA-600036 > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] carbon nanotube - ifnite in length ?
On 9/26/13 8:39 AM, Steven Neumann wrote: Dear Gmx Users, I have my carbon nanotube and I wish to make it infinite in lenght. Which mdp options whall be used? pbc = xy and z is the infinite dimension? another issue: Would you apply bonds between carbon atoms within the nanotube or constraints using LINCS? Which of them is less computationally expensive for the run? Use "pbc = xyz" in conjunction with "periodic_molecules = yes" otherwise the topology gets messed up trying to form unreasonable bonds. The periodic_molecules keyword in the .mdp allows for bonds to be maintained over PBC. I remember a very old post somewhere in the archive that said one should not apply pressure coupling along the axis of the nanotube, due to some difficulties with maintaining the bonded geometry, but since I have never done CNT simulations, take the fact that I'm just repeating what I've heard for what it's worth :) Constraints always come with the cost of communication, so I would imagine harmonic bonds are "less expensive." I really don't see constraints as a limiting factor for performance, though. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] carbon nanotube - ifnite in length ?
I am just curious why the system would explode without "periodic_molecules = yes". If the PBC procedure is applied before harmonic bond potential is calculated, than the opposite nanotube atoms should be (already) seen as neighboring. This looks the same as the solvent molecule, one atom of which crossed the box boundary. No? Dr. Vitaly V. Chaban On Thu, Sep 26, 2013 at 3:59 PM, Justin Lemkul wrote: > > > On 9/26/13 8:39 AM, Steven Neumann wrote: >> >> Dear Gmx Users, >> >> I have my carbon nanotube and I wish to make it infinite in lenght. Which >> mdp options whall be used? pbc = xy and z is the infinite dimension? >> another issue: Would you apply bonds between carbon atoms within the >> nanotube or constraints using LINCS? Which of them is less computationally >> expensive for the run? >> > > Use "pbc = xyz" in conjunction with "periodic_molecules = yes" otherwise the > topology gets messed up trying to form unreasonable bonds. The > periodic_molecules keyword in the .mdp allows for bonds to be maintained > over PBC. > > I remember a very old post somewhere in the archive that said one should not > apply pressure coupling along the axis of the nanotube, due to some > difficulties with maintaining the bonded geometry, but since I have never > done CNT simulations, take the fact that I'm just repeating what I've heard > for what it's worth :) > > Constraints always come with the cost of communication, so I would imagine > harmonic bonds are "less expensive." I really don't see constraints as a > limiting factor for performance, though. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > == > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Preprocessor statements
Hi guys, Is it possible to specify in the topol.top file preprocessor statements, so that you can stop the simulation prematurely? I pull two molecules together and I'd like to stop the simulation if the center of mass distance of the molecules is less than xx nm. Best, grita -- View this message in context: http://gromacs.5086.x6.nabble.com/Preprocessor-statements-tp5011469.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Preprocessor statements
Unlikely possible... But yeah, the feature might be handy. Dr. Vitaly V. Chaban On Thu, Sep 26, 2013 at 4:20 PM, grita wrote: > Hi guys, > > Is it possible to specify in the topol.top file preprocessor statements, so > that you can stop the simulation prematurely? > > I pull two molecules together and I'd like to stop the simulation if the > center of mass distance of the molecules is less than xx nm. > > Best, > grita > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Preprocessor-statements-tp5011469.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] carbon nanotube - ifnite in length ?
Thank you for this. And also I wish to attach a chain to my nanotube so they will be both able to move together. Is that a matter of distance restraints between nanotube atom and first atom of my chain or again - LINCS? Both chain and nanotube are made of the same type of 8 type of atoms. Please, advise. Steven On Thu, Sep 26, 2013 at 3:19 PM, Dr. Vitaly Chaban wrote: > I am just curious why the system would explode without > "periodic_molecules = yes". If the PBC procedure is applied before > harmonic bond potential is calculated, than the opposite nanotube > atoms should be (already) seen as neighboring. This looks the same as > the solvent molecule, one atom of which crossed the box boundary. > > No? > > > > Dr. Vitaly V. Chaban > > > On Thu, Sep 26, 2013 at 3:59 PM, Justin Lemkul wrote: > > > > > > On 9/26/13 8:39 AM, Steven Neumann wrote: > >> > >> Dear Gmx Users, > >> > >> I have my carbon nanotube and I wish to make it infinite in lenght. > Which > >> mdp options whall be used? pbc = xy and z is the infinite dimension? > >> another issue: Would you apply bonds between carbon atoms within the > >> nanotube or constraints using LINCS? Which of them is less > computationally > >> expensive for the run? > >> > > > > Use "pbc = xyz" in conjunction with "periodic_molecules = yes" otherwise > the > > topology gets messed up trying to form unreasonable bonds. The > > periodic_molecules keyword in the .mdp allows for bonds to be maintained > > over PBC. > > > > I remember a very old post somewhere in the archive that said one should > not > > apply pressure coupling along the axis of the nanotube, due to some > > difficulties with maintaining the bonded geometry, but since I have never > > done CNT simulations, take the fact that I'm just repeating what I've > heard > > for what it's worth :) > > > > Constraints always come with the cost of communication, so I would > imagine > > harmonic bonds are "less expensive." I really don't see constraints as a > > limiting factor for performance, though. > > > > -Justin > > > > -- > > == > > > > Justin A. Lemkul, Ph.D. > > Postdoctoral Fellow > > > > Department of Pharmaceutical Sciences > > School of Pharmacy > > Health Sciences Facility II, Room 601 > > University of Maryland, Baltimore > > 20 Penn St. > > Baltimore, MD 21201 > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > > == > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Preprocessor statements
No, there's no way to do that. But you can monitor the output trajectory file yourself, live. Mark On Thu, Sep 26, 2013 at 4:49 PM, Dr. Vitaly Chaban wrote: > Unlikely possible... But yeah, the feature might be handy. > > > Dr. Vitaly V. Chaban > > > On Thu, Sep 26, 2013 at 4:20 PM, grita wrote: >> Hi guys, >> >> Is it possible to specify in the topol.top file preprocessor statements, so >> that you can stop the simulation prematurely? >> >> I pull two molecules together and I'd like to stop the simulation if the >> center of mass distance of the molecules is less than xx nm. >> >> Best, >> grita >> >> -- >> View this message in context: >> http://gromacs.5086.x6.nabble.com/Preprocessor-statements-tp5011469.html >> Sent from the GROMACS Users Forum mailing list archive at Nabble.com. >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat after trjconv
Dear Sir, Thanks for the quick reply. I accidentally lost one of my raw .xtc files. But I have the noPBC xtc file. So, when ever I extend my simulation, first I am removing PBC then concatenating it with existing noPBC xtc file. Is it fine?? On Thu, Sep 26, 2013 at 7:13 PM, Dr. Vitaly Chaban wrote: > I do not think that I ever tried myself, but is seems all the same. > Why do you ask? > > > Dr. Vitaly V. Chaban > > > On Thu, Sep 26, 2013 at 3:40 PM, Venkat Reddy wrote: > > Dear all, > > I have a basic doubt. Is there any difference between the two processes > > where > > 1) I concatenate the trajectories and do trjconv to remove PBC, which is > a > > default process > > 2) Do trjconv on all the xtc files separately and then concatenate them. > > > > Thank you for your time > > > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat after trjconv
Hi Venkat, It depends on what you mean with "removing pbc". Cheers, Tsjerk On Sep 26, 2013 5:21 PM, "Venkat Reddy" wrote: Dear Sir, Thanks for the quick reply. I accidentally lost one of my raw .xtc files. But I have the noPBC xtc file. So, when ever I extend my simulation, first I am removing PBC then concatenating it with existing noPBC xtc file. Is it fine?? On Thu, Sep 26, 2013 at 7:13 PM, Dr. Vitaly Chaban wrote: > I do not think that I ever tried myself, but is seems all the same. > Why do you ask? > > > Dr. V... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] carbon nanotube - ifnite in length ?
Steven - I would use a simple harmonic bond. Dr. Vitaly V. Chaban On Thu, Sep 26, 2013 at 5:12 PM, Steven Neumann wrote: > Thank you for this. And also I wish to attach a chain to my nanotube so they > will be both able to move together. Is that a matter of distance restraints > between nanotube atom and first atom of my chain or again - LINCS? Both > chain and nanotube are made of the same type of 8 type of atoms. Please, > advise. > > Steven > > > On Thu, Sep 26, 2013 at 3:19 PM, Dr. Vitaly Chaban > wrote: >> >> I am just curious why the system would explode without >> "periodic_molecules = yes". If the PBC procedure is applied before >> harmonic bond potential is calculated, than the opposite nanotube >> atoms should be (already) seen as neighboring. This looks the same as >> the solvent molecule, one atom of which crossed the box boundary. >> >> No? >> >> >> >> Dr. Vitaly V. Chaban >> >> >> On Thu, Sep 26, 2013 at 3:59 PM, Justin Lemkul wrote: >> > >> > >> > On 9/26/13 8:39 AM, Steven Neumann wrote: >> >> >> >> Dear Gmx Users, >> >> >> >> I have my carbon nanotube and I wish to make it infinite in lenght. >> >> Which >> >> mdp options whall be used? pbc = xy and z is the infinite dimension? >> >> another issue: Would you apply bonds between carbon atoms within the >> >> nanotube or constraints using LINCS? Which of them is less >> >> computationally >> >> expensive for the run? >> >> >> > >> > Use "pbc = xyz" in conjunction with "periodic_molecules = yes" otherwise >> > the >> > topology gets messed up trying to form unreasonable bonds. The >> > periodic_molecules keyword in the .mdp allows for bonds to be maintained >> > over PBC. >> > >> > I remember a very old post somewhere in the archive that said one should >> > not >> > apply pressure coupling along the axis of the nanotube, due to some >> > difficulties with maintaining the bonded geometry, but since I have >> > never >> > done CNT simulations, take the fact that I'm just repeating what I've >> > heard >> > for what it's worth :) >> > >> > Constraints always come with the cost of communication, so I would >> > imagine >> > harmonic bonds are "less expensive." I really don't see constraints as >> > a >> > limiting factor for performance, though. >> > >> > -Justin >> > >> > -- >> > == >> > >> > Justin A. Lemkul, Ph.D. >> > Postdoctoral Fellow >> > >> > Department of Pharmaceutical Sciences >> > School of Pharmacy >> > Health Sciences Facility II, Room 601 >> > University of Maryland, Baltimore >> > 20 Penn St. >> > Baltimore, MD 21201 >> > >> > jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> > >> > == >> > -- >> > gmx-users mailing listgmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> > * Please don't post (un)subscribe requests to the list. Use the www >> > interface or send it to gmx-users-requ...@gromacs.org. >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] per mol of what?
Hi when calculating an energy contribution using g_energy, the units specified in the plots, as well as in the output tables, are kJ/mol. This happens even when the -nmol flag is missing (so nmol=1). On the other hand, the energy units in gromacs are kJ/mol. So I guess that when a term (a dihedral or whatever) is added to the total potential it refers to kJ per mol of that term. The total energy of a system comes from the sum of all the potential energy plus the kinetic energy contributions and the units are again kJ/mol. Then, how should I understand that? kJ per mol of system contained in the unit cell? Let me put an example: I have 6 solute molecules solvated in 5000 SPC waters and I use g_energy to determine the coulombic contribution to the solute-water interactions or to the solute-solute interactions as a function of time. The result is given in kJ/mol. If I want to determine the same contribution(s) per mole of solute should I divide by 6 maintaining the units as kJ/mol? Then, if I have the same system with 12 solute molecules, would make sense to compare the equivalent contribution divided by 12? After taking a look to the code and to the results for a couple of systems I think this is correct but the answer is too basic and important just to assume that I am right so I would be happy if I have a confirmation. Thanks in advance, Ángel. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Writing periodic image coordinates.
Dear users, For some analysis I require the 27 periodic images of the system I ran the simulation for. Kindly let me know how can it be written to a pdb file. Thanking you Regards Kavya -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat after trjconv
Dear Tsjerk sir, I used trjconv -pbc mol -ur compact options. On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar wrote: > Hi Venkat, > > It depends on what you mean with "removing pbc". > > Cheers, > > Tsjerk > > On Sep 26, 2013 5:21 PM, "Venkat Reddy" wrote: > > Dear Sir, > Thanks for the quick reply. > I accidentally lost one of my raw .xtc files. But I have the noPBC xtc > file. So, when ever I extend my simulation, first I am removing PBC then > concatenating it with existing noPBC xtc file. Is it fine?? > > > On Thu, Sep 26, 2013 at 7:13 PM, Dr. Vitaly Chaban >wrote: > > > I do not think that I ever tried myself, but is seems all the same. > Why > do you ask? > > > Dr. V... > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat after trjconv
Hi Venkat, These options are 'frame intrinsic' or 'history independent', unlike -pbc nojump. Cheers, Tsjerk On Sep 26, 2013 6:46 PM, "Venkat Reddy" wrote: Dear Tsjerk sir, I used trjconv -pbc mol -ur compact options. On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar wrote: > Hi Venkat, > > It... > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/g... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial
Dear Users: Has anyone successfully run the free energy tutorial at http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy ? I just tried it and I get a segmentation fault immediately (see output at the end of this post). I get a segfault with both 4.6.3 and 4.6.1. Note that if I modify the .mdp file to set free-energy = no , then the simulation runs just fine. (I have, of course, set init-lambda-state in the .mdp file that I downloaded from the aforementioned site and I get a segfault with any value of init-lambda-state from 0 to 8). gpc-f103n084-$ mdrun -nt 1 -deffnm ethanol.1 -dhdl ethanol.1.dhdl.xvg :-) G R O M A C S (-: GROup of MAchos and Cynical Suckers :-) VERSION 4.6.3 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University & The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) mdrun (-: Option Filename Type Description -s ethanol.1.tpr InputRun input file: tpr tpb tpa -o ethanol.1.trr Output Full precision trajectory: trr trj cpt -x ethanol.1.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi ethanol.1.cpt Input, Opt. Checkpoint file -cpo ethanol.1.cpt Output, Opt. Checkpoint file -c ethanol.1.gro Output Structure file: gro g96 pdb etc. -e ethanol.1.edr Output Energy file -g ethanol.1.log Output Log file -dhdl ethanol.1.dhdl.xvg Output, Opt! xvgr/xmgr file -field ethanol.1.xvg Output, Opt. xvgr/xmgr file -table ethanol.1.xvg Input, Opt. xvgr/xmgr file -tabletf ethanol.1.xvg Input, Opt. xvgr/xmgr file -tablep ethanol.1.xvg Input, Opt. xvgr/xmgr file -tableb ethanol.1.xvg Input, Opt. xvgr/xmgr file -rerun ethanol.1.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpi ethanol.1.xvg Output, Opt. xvgr/xmgr file -tpid ethanol.1.xvg Output, Opt. xvgr/xmgr file -ei ethanol.1.edi Input, Opt. ED sampling input -eo ethanol.1.xvg Output, Opt. xvgr/xmgr file -j ethanol.1.gct Input, Opt. General coupling stuff -jo ethanol.1.gct Output, Opt. General coupling stuff -ffout ethanol.1.xvg Output, Opt. xvgr/xmgr file -devout ethanol.1.xvg Output, Opt. xvgr/xmgr file -runav ethanol.1.xvg Output, Opt. xvgr/xmgr file -px ethanol.1.xvg Output, Opt. xvgr/xmgr file -pf ethanol.1.xvg Output, Opt. xvgr/xmgr file -ro ethanol.1.xvg Output, Opt. xvgr/xmgr file -ra ethanol.1.log Output, Opt. Log file -rs ethanol.1.log Output, Opt. Log file -rt ethanol.1.log Output, Opt. Log file -mtx ethanol.1.mtx Output, Opt. Hessian matrix -dn ethanol.1.ndx Output, Opt. Index file -multidir ethanol.1 Input, Opt., Mult. Run directory -membed ethanol.1.dat Input, Opt. Generic data file -mp ethanol.1.top Input, Opt. Topology file -mn ethanol.1.ndx Input, Opt. Index file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -deffnm string ethanol.1 Set the default filename for all file options -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]pd bool no Use particle decompostion -dd vector 0 0 0 Domain decomposition grid, 0 is optimize -ddorder enum interleave DD node order: interleave, pp_pme or cartesian -npmeint-1 Number of separate nodes to be used for PME, -1 is guess -nt int1 Total number of threads to start (0 is guess) -ntmpi int0 Number of thread-MPI threads to start (0 is guess) -ntomp int0 Number of OpenMP threads per MPI process/thread to start (0 is guess) -ntomp_pme int0 Number of OpenMP threads per MPI process/t
Re: [gmx-users] Writing periodic image coordinates.
Hi Kavya, genconf -nbox 3 3 3 Cheers, Tsjerk On Thu, Sep 26, 2013 at 6:24 PM, Kavyashree M wrote: > Dear users, > > For some analysis I require the 27 periodic images > of the system I ran the simulation for. Kindly let me > know how can it be written to a pdb file. > > Thanking you > Regards > Kavya > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] per mol of what?
Hi Ángel, kJ per mol of system contained in the unit cell? > > Exactly. As if whatever is in there is one 'molecule' (-nmol 1). Adios! Tsjerk -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] carbon nanotube - ifnite in length ?
On 9/26/13 12:05 PM, Dr. Vitaly Chaban wrote: Steven - I would use a simple harmonic bond. Note that either in the case of the distance restraint or harmonic interaction approach, both the CNT and the molecule to which it is tethered need to be in the same [moleculetype], so run pdb2gmx (or whatever you are using) with care. -Justin Dr. Vitaly V. Chaban On Thu, Sep 26, 2013 at 5:12 PM, Steven Neumann wrote: Thank you for this. And also I wish to attach a chain to my nanotube so they will be both able to move together. Is that a matter of distance restraints between nanotube atom and first atom of my chain or again - LINCS? Both chain and nanotube are made of the same type of 8 type of atoms. Please, advise. Steven On Thu, Sep 26, 2013 at 3:19 PM, Dr. Vitaly Chaban wrote: I am just curious why the system would explode without "periodic_molecules = yes". If the PBC procedure is applied before harmonic bond potential is calculated, than the opposite nanotube atoms should be (already) seen as neighboring. This looks the same as the solvent molecule, one atom of which crossed the box boundary. No? Dr. Vitaly V. Chaban On Thu, Sep 26, 2013 at 3:59 PM, Justin Lemkul wrote: On 9/26/13 8:39 AM, Steven Neumann wrote: Dear Gmx Users, I have my carbon nanotube and I wish to make it infinite in lenght. Which mdp options whall be used? pbc = xy and z is the infinite dimension? another issue: Would you apply bonds between carbon atoms within the nanotube or constraints using LINCS? Which of them is less computationally expensive for the run? Use "pbc = xyz" in conjunction with "periodic_molecules = yes" otherwise the topology gets messed up trying to form unreasonable bonds. The periodic_molecules keyword in the .mdp allows for bonds to be maintained over PBC. I remember a very old post somewhere in the archive that said one should not apply pressure coupling along the axis of the nanotube, due to some difficulties with maintaining the bonded geometry, but since I have never done CNT simulations, take the fact that I'm just repeating what I've heard for what it's worth :) Constraints always come with the cost of communication, so I would imagine harmonic bonds are "less expensive." I really don't see constraints as a limiting factor for performance, though. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] carbon nanotube - ifnite in length ?
On 9/26/13 10:19 AM, Dr. Vitaly Chaban wrote: I am just curious why the system would explode without "periodic_molecules = yes". If the PBC procedure is applied before harmonic bond potential is calculated, than the opposite nanotube atoms should be (already) seen as neighboring. This looks the same as the solvent molecule, one atom of which crossed the box boundary. No? Without setting the periodic_molecules keyword, mdrun tries to assemble all the bonds within the unit cell. Given that a bond between atoms at either end of the box would be very unfavorable, it would distort the system considerably, or fail altogether if using constraints. Bonds only span PBC when instructed with periodic_molecules. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Membrane simulation with OPLS ff.
Dear GMX users: Is OPLSAA forcefield data already available for POPC membranes. I am interested in simulation of proteins in POPC membrane. Thank you. Best Regards Karthi. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial
I found the -multi version of that tutorial a bit temperamental... Michael Shirts suggested that double precision is more reliable for expanded ensemble. Hopefully he can chime in in a day or two. Mark On Thu, Sep 26, 2013 at 9:00 PM, Christopher Neale wrote: > Dear Users: > > Has anyone successfully run the free energy tutorial at > http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy > ? > > I just tried it and I get a segmentation fault immediately (see output at the > end of this post). > > I get a segfault with both 4.6.3 and 4.6.1. > > Note that if I modify the .mdp file to set free-energy = no , then the > simulation runs just fine. (I have, of course, set init-lambda-state in the > .mdp file that I downloaded from the aforementioned site and I get a segfault > with any value of init-lambda-state from 0 to 8). > > gpc-f103n084-$ mdrun -nt 1 -deffnm ethanol.1 -dhdl ethanol.1.dhdl.xvg > :-) G R O M A C S (-: > > GROup of MAchos and Cynical Suckers > > :-) VERSION 4.6.3 (-: > > Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, >Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, > Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, > Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, >Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, > Michael Shirts, Alfons Sijbers, Peter Tieleman, > >Berk Hess, David van der Spoel, and Erik Lindahl. > >Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2012,2013, The GROMACS development team at > Uppsala University & The Royal Institute of Technology, Sweden. > check out http://www.gromacs.org for more information. > > This program is free software; you can redistribute it and/or >modify it under the terms of the GNU Lesser General Public License > as published by the Free Software Foundation; either version 2.1 > of the License, or (at your option) any later version. > > :-) mdrun (-: > > Option Filename Type Description > > -s ethanol.1.tpr InputRun input file: tpr tpb tpa > -o ethanol.1.trr Output Full precision trajectory: trr trj cpt > -x ethanol.1.xtc Output, Opt. Compressed trajectory (portable xdr format) > -cpi ethanol.1.cpt Input, Opt. Checkpoint file > -cpo ethanol.1.cpt Output, Opt. Checkpoint file > -c ethanol.1.gro Output Structure file: gro g96 pdb etc. > -e ethanol.1.edr Output Energy file > -g ethanol.1.log Output Log file > -dhdl ethanol.1.dhdl.xvg Output, Opt! xvgr/xmgr file > -field ethanol.1.xvg Output, Opt. xvgr/xmgr file > -table ethanol.1.xvg Input, Opt. xvgr/xmgr file > -tabletf ethanol.1.xvg Input, Opt. xvgr/xmgr file > -tablep ethanol.1.xvg Input, Opt. xvgr/xmgr file > -tableb ethanol.1.xvg Input, Opt. xvgr/xmgr file > -rerun ethanol.1.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt > -tpi ethanol.1.xvg Output, Opt. xvgr/xmgr file > -tpid ethanol.1.xvg Output, Opt. xvgr/xmgr file > -ei ethanol.1.edi Input, Opt. ED sampling input > -eo ethanol.1.xvg Output, Opt. xvgr/xmgr file > -j ethanol.1.gct Input, Opt. General coupling stuff > -jo ethanol.1.gct Output, Opt. General coupling stuff > -ffout ethanol.1.xvg Output, Opt. xvgr/xmgr file > -devout ethanol.1.xvg Output, Opt. xvgr/xmgr file > -runav ethanol.1.xvg Output, Opt. xvgr/xmgr file > -px ethanol.1.xvg Output, Opt. xvgr/xmgr file > -pf ethanol.1.xvg Output, Opt. xvgr/xmgr file > -ro ethanol.1.xvg Output, Opt. xvgr/xmgr file > -ra ethanol.1.log Output, Opt. Log file > -rs ethanol.1.log Output, Opt. Log file > -rt ethanol.1.log Output, Opt. Log file > -mtx ethanol.1.mtx Output, Opt. Hessian matrix > -dn ethanol.1.ndx Output, Opt. Index file > -multidir ethanol.1 Input, Opt., Mult. Run directory > -membed ethanol.1.dat Input, Opt. Generic data file > -mp ethanol.1.top Input, Opt. Topology file > -mn ethanol.1.ndx Input, Opt. Index file > > Option Type Value Description > -- > -[no]h bool no Print help info and quit > -[no]version bool no Print version info and quit > -niceint0 Set the nicelevel > -deffnm string ethanol.1 Set the default filename for all file options > -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none > -[no]pd bool no Use particle decompostion > -dd vector 0 0 0 Domain decomposition grid, 0 is optimize > -ddorder enum interleave DD node order: interleave, pp_pme or cartesian > -npmeint-1
[gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial
Thank you Mark. I actually found that it crashed wihout the -multi part (no hamiltonian exchange). The command that I used was: mdrun -nt 1 -deffnm ethanol.1 -dhdl ethanol.1.dhdl.xvg If I use the double precision version, there is no segfault. That's a working solution, but it is worrysome. Thank you, Chris. -- original message -- I found the -multi version of that tutorial a bit temperamental... Michael Shirts suggested that double precision is more reliable for expanded ensemble. Hopefully he can chime in in a day or two. Mark On Thu, Sep 26, 2013 at 9:00 PM, Christopher Neale wrote: > Dear Users: > > Has anyone successfully run the free energy tutorial at > http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy > ? > > I just tried it and I get a segmentation fault immediately (see output at the > end of this post). > > I get a segfault with both 4.6.3 and 4.6.1. > > Note that if I modify the .mdp file to set free-energy = no , then the > simulation runs just fine. (I have, of course, set init-lambda-state in the > .mdp file that I downloaded from the aforementioned site and I get a segfault > with any value of init-lambda-state from 0 to 8). > > gpc-f103n084-$ mdrun -nt 1 -deffnm ethanol.1 -dhdl ethanol.1.dhdl.xvg > :-) G R O M A C S (-: > > GROup of MAchos and Cynical Suckers > > :-) VERSION 4.6.3 (-: > > Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, >Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, > Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, > Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, >Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, > Michael Shirts, Alfons Sijbers, Peter Tieleman, > >Berk Hess, David van der Spoel, and Erik Lindahl. > >Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2012,2013, The GROMACS development team at > Uppsala University & The Royal Institute of Technology, Sweden. > check out http://www.gromacs.org for more information. > > This program is free software; you can redistribute it and/or >modify it under the terms of the GNU Lesser General Public License > as published by the Free Software Foundation; either version 2.1 > of the License, or (at your option) any later version. > > :-) mdrun (-: > > Option Filename Type Description > > -s ethanol.1.tpr InputRun input file: tpr tpb tpa > -o ethanol.1.trr Output Full precision trajectory: trr trj cpt > -x ethanol.1.xtc Output, Opt. Compressed trajectory (portable xdr format) > -cpi ethanol.1.cpt Input, Opt. Checkpoint file > -cpo ethanol.1.cpt Output, Opt. Checkpoint file > -c ethanol.1.gro Output Structure file: gro g96 pdb etc. > -e ethanol.1.edr Output Energy file > -g ethanol.1.log Output Log file > -dhdl ethanol.1.dhdl.xvg Output, Opt! xvgr/xmgr file > -field ethanol.1.xvg Output, Opt. xvgr/xmgr file > -table ethanol.1.xvg Input, Opt. xvgr/xmgr file > -tabletf ethanol.1.xvg Input, Opt. xvgr/xmgr file > -tablep ethanol.1.xvg Input, Opt. xvgr/xmgr file > -tableb ethanol.1.xvg Input, Opt. xvgr/xmgr file > -rerun ethanol.1.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt > -tpi ethanol.1.xvg Output, Opt. xvgr/xmgr file > -tpid ethanol.1.xvg Output, Opt. xvgr/xmgr file > -ei ethanol.1.edi Input, Opt. ED sampling input > -eo ethanol.1.xvg Output, Opt. xvgr/xmgr file > -j ethanol.1.gct Input, Opt. General coupling stuff > -jo ethanol.1.gct Output, Opt. General coupling stuff > -ffout ethanol.1.xvg Output, Opt. xvgr/xmgr file > -devout ethanol.1.xvg Output, Opt. xvgr/xmgr file > -runav ethanol.1.xvg Output, Opt. xvgr/xmgr file > -px ethanol.1.xvg Output, Opt. xvgr/xmgr file > -pf ethanol.1.xvg Output, Opt. xvgr/xmgr file > -ro ethanol.1.xvg Output, Opt. xvgr/xmgr file > -ra ethanol.1.log Output, Opt. Log file > -rs ethanol.1.log Output, Opt. Log file > -rt ethanol.1.log Output, Opt. Log file > -mtx ethanol.1.mtx Output, Opt. Hessian matrix > -dn ethanol.1.ndx Output, Opt. Index file > -multidir ethanol.1 Input, Opt., Mult. Run directory > -membed ethanol.1.dat Input, Opt. Generic data file > -mp ethanol.1.top Input, Opt. Topology file > -mn ethanol.1.ndx Input, Opt. Index file > > Option Type Value Description > -- > -[no]h bool no Print help info and quit > -[no]version bool no Print version info and quit > -niceint0 Set the nicelevel > -deffnm string ethanol.1 Set the defa
Re: [gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial
Just to be clear, is this the expanded ensemble version of the calculation? On Thu, Sep 26, 2013 at 5:25 PM, Mark Abraham wrote: > I found the -multi version of that tutorial a bit temperamental... > Michael Shirts suggested that double precision is more reliable for > expanded ensemble. Hopefully he can chime in in a day or two. > > Mark > > On Thu, Sep 26, 2013 at 9:00 PM, Christopher Neale > wrote: >> Dear Users: >> >> Has anyone successfully run the free energy tutorial at >> http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy >> ? >> >> I just tried it and I get a segmentation fault immediately (see output at >> the end of this post). >> >> I get a segfault with both 4.6.3 and 4.6.1. >> >> Note that if I modify the .mdp file to set free-energy = no , then the >> simulation runs just fine. (I have, of course, set init-lambda-state in the >> .mdp file that I downloaded from the aforementioned site and I get a >> segfault with any value of init-lambda-state from 0 to 8). >> >> gpc-f103n084-$ mdrun -nt 1 -deffnm ethanol.1 -dhdl ethanol.1.dhdl.xvg >> :-) G R O M A C S (-: >> >> GROup of MAchos and Cynical Suckers >> >> :-) VERSION 4.6.3 (-: >> >> Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, >>Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, >> Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, >> Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, >>Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, >> Michael Shirts, Alfons Sijbers, Peter Tieleman, >> >>Berk Hess, David van der Spoel, and Erik Lindahl. >> >>Copyright (c) 1991-2000, University of Groningen, The Netherlands. >> Copyright (c) 2001-2012,2013, The GROMACS development team at >> Uppsala University & The Royal Institute of Technology, Sweden. >> check out http://www.gromacs.org for more information. >> >> This program is free software; you can redistribute it and/or >>modify it under the terms of the GNU Lesser General Public License >> as published by the Free Software Foundation; either version 2.1 >> of the License, or (at your option) any later version. >> >> :-) mdrun (-: >> >> Option Filename Type Description >> >> -s ethanol.1.tpr InputRun input file: tpr tpb tpa >> -o ethanol.1.trr Output Full precision trajectory: trr trj cpt >> -x ethanol.1.xtc Output, Opt. Compressed trajectory (portable xdr format) >> -cpi ethanol.1.cpt Input, Opt. Checkpoint file >> -cpo ethanol.1.cpt Output, Opt. Checkpoint file >> -c ethanol.1.gro Output Structure file: gro g96 pdb etc. >> -e ethanol.1.edr Output Energy file >> -g ethanol.1.log Output Log file >> -dhdl ethanol.1.dhdl.xvg Output, Opt! xvgr/xmgr file >> -field ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -table ethanol.1.xvg Input, Opt. xvgr/xmgr file >> -tabletf ethanol.1.xvg Input, Opt. xvgr/xmgr file >> -tablep ethanol.1.xvg Input, Opt. xvgr/xmgr file >> -tableb ethanol.1.xvg Input, Opt. xvgr/xmgr file >> -rerun ethanol.1.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt >> -tpi ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -tpid ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -ei ethanol.1.edi Input, Opt. ED sampling input >> -eo ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -j ethanol.1.gct Input, Opt. General coupling stuff >> -jo ethanol.1.gct Output, Opt. General coupling stuff >> -ffout ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -devout ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -runav ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -px ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -pf ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -ro ethanol.1.xvg Output, Opt. xvgr/xmgr file >> -ra ethanol.1.log Output, Opt. Log file >> -rs ethanol.1.log Output, Opt. Log file >> -rt ethanol.1.log Output, Opt. Log file >> -mtx ethanol.1.mtx Output, Opt. Hessian matrix >> -dn ethanol.1.ndx Output, Opt. Index file >> -multidir ethanol.1 Input, Opt., Mult. Run directory >> -membed ethanol.1.dat Input, Opt. Generic data file >> -mp ethanol.1.top Input, Opt. Topology file >> -mn ethanol.1.ndx Input, Opt. Index file >> >> Option Type Value Description >> -- >> -[no]h bool no Print help info and quit >> -[no]version bool no Print version info and quit >> -niceint0 Set the nicelevel >> -deffnm string ethanol.1 Set the default filename for all file options >> -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
[gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial
My mistake I still get a segfault even when using double precision. (EM doesn't help, nor does switching to Berendsen pressure coupling). Note that I can stop the segfault when running at init-lambda-state = 0 if I set: couple-lambda0 = none couple-lambda1 = none instead of couple-lambda0 = vdw-q couple-lambda1 = none This looks like http://bugzilla.gromacs.org/issues/1306 Thank you, Chris. -- original message -- Thank you Mark. I actually found that it crashed wihout the -multi part (no hamiltonian exchange). The command that I used was: mdrun -nt 1 -deffnm ethanol.1 -dhdl ethanol.1.dhdl.xvg If I use the double precision version, there is no segfault. That's a working solution, but it is worrysome. Thank you, Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial
No, this is not the expanded ensemble version. It's the initial "Running the calculation with Gromacs" section straight out of http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy I get the segfault with a single run (at any of the 9 individual lambda values). -- original message -- Just to be clear, is this the expanded ensemble version of the calculation? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial
I thought I had just managed to solve the issue :) If you look at the soft core parameters, there are two types listed -- one with sc-r-power = 48, and one with sc-r-power = 6. The sc-r-power are more stable with single precision calculations. I have changed the files on the website to make the single precision ones the default. Expanded.mdp warned about the issues with precision, but left the sc-r-power in place; the Ethanol.mdp did not warn about the potential issue. Now both include the more efficient path commented out. NOTE that this means the exact numbers of the tutorials are not quite right anymore; the process is unchanged, as is the final answer, but the intermediate dG's will be slightly different. However, I need to redo them anyway to make them easier in the next 1-2 weeks, so I will update them then. If it still fails with double, that's a different issue -- because I'm running them fine with double. On Thu, Sep 26, 2013 at 6:32 PM, Christopher Neale wrote: > My mistake I still get a segfault even when using double precision. (EM > doesn't help, nor does switching to Berendsen pressure coupling). > > Note that I can stop the segfault when running at init-lambda-state = 0 if I > set: > > couple-lambda0 = none > couple-lambda1 = none > > instead of > > couple-lambda0 = vdw-q > couple-lambda1 = none > > This looks like http://bugzilla.gromacs.org/issues/1306 > > Thank you, > Chris. > > -- original message -- > > Thank you Mark. > > I actually found that it crashed wihout the -multi part (no hamiltonian > exchange). > The command that I used was: mdrun -nt 1 -deffnm ethanol.1 -dhdl > ethanol.1.dhdl.xvg > > If I use the double precision version, there is no segfault. That's a working > solution, but it is worrysome. > > Thank you, > Chris. > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial
And with this change, single is running fine as well. This was a known issue, but was only documented in the expanded.mdp files, which was an oversight. After this, I switched so the default is less likely to cause problems. Because of some theory improvements developed in the group in free energy calculation pathways, the sc-r-power=48 pathway will now be phased out anyway by 5.1. On Thu, Sep 26, 2013 at 6:37 PM, Michael Shirts wrote: > I thought I had just managed to solve the issue :) > > If you look at the soft core parameters, there are two types listed -- > one with sc-r-power = 48, and one with sc-r-power = 6. The sc-r-power > are more stable with single precision calculations. > > I have changed the files on the website to make the single precision > ones the default. Expanded.mdp warned about the issues with > precision, but left the sc-r-power in place; the Ethanol.mdp did not > warn about the potential issue. Now both include the more efficient > path commented out. > > NOTE that this means the exact numbers of the tutorials are not quite > right anymore; the process is unchanged, as is the final answer, but > the intermediate dG's will be slightly different. > > However, I need to redo them anyway to make them easier in the next > 1-2 weeks, so I will update them then. > > If it still fails with double, that's a different issue -- because I'm > running them fine with double. > > > > > > On Thu, Sep 26, 2013 at 6:32 PM, Christopher Neale > wrote: >> My mistake I still get a segfault even when using double precision. (EM >> doesn't help, nor does switching to Berendsen pressure coupling). >> >> Note that I can stop the segfault when running at init-lambda-state = 0 if I >> set: >> >> couple-lambda0 = none >> couple-lambda1 = none >> >> instead of >> >> couple-lambda0 = vdw-q >> couple-lambda1 = none >> >> This looks like http://bugzilla.gromacs.org/issues/1306 >> >> Thank you, >> Chris. >> >> -- original message -- >> >> Thank you Mark. >> >> I actually found that it crashed wihout the -multi part (no hamiltonian >> exchange). >> The command that I used was: mdrun -nt 1 -deffnm ethanol.1 -dhdl >> ethanol.1.dhdl.xvg >> >> If I use the double precision version, there is no segfault. That's a >> working solution, but it is worrysome. >> >> Thank you, >> Chris. >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial
Agreed, the following parameters do not segfault in single or double precision: sc-alpha = 0.5 sc-power = 1 sc-r-power = 6 Same goes for http://bugzilla.gromacs.org/issues/1306 The following parameters give a segfault in single precision but are ok in double precision sc-alpha = 0.001 sc-power = 1 sc-r-power = 48 Same goes for http://bugzilla.gromacs.org/issues/1306 Sorry for the confusion earlier. I was using a compilation that I thought was double precision but it was actually single. Recompiling in double precision gave me the stability outlined above. Thank you for your assitance Mark and Michael. Chris. -- original message -- Michael Shirts mrshirts at gmail.com Fri Sep 27 00:41:17 CEST 2013 Previous message: [gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial Next message: [gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] And with this change, single is running fine as well. This was a known issue, but was only documented in the expanded.mdp files, which was an oversight. After this, I switched so the default is less likely to cause problems. Because of some theory improvements developed in the group in free energy calculation pathways, the sc-r-power=48 pathway will now be phased out anyway by 5.1. On Thu, Sep 26, 2013 at 6:37 PM, Michael Shirts wrote: > I thought I had just managed to solve the issue :) > > If you look at the soft core parameters, there are two types listed -- > one with sc-r-power = 48, and one with sc-r-power = 6. The sc-r-power > are more stable with single precision calculations. > > I have changed the files on the website to make the single precision > ones the default. Expanded.mdp warned about the issues with > precision, but left the sc-r-power in place; the Ethanol.mdp did not > warn about the potential issue. Now both include the more efficient > path commented out. > > NOTE that this means the exact numbers of the tutorials are not quite > right anymore; the process is unchanged, as is the final answer, but > the intermediate dG's will be slightly different. > > However, I need to redo them anyway to make them easier in the next > 1-2 weeks, so I will update them then. > > If it still fails with double, that's a different issue -- because I'm > running them fine with double. > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial
Sounds like we've resolved all the confusion. Thanks for prompt help in making this clearer and better. On Thu, Sep 26, 2013 at 7:01 PM, Christopher Neale wrote: > Agreed, the following parameters do not segfault in single or double > precision: > sc-alpha = 0.5 > sc-power = 1 > sc-r-power = 6 > Same goes for http://bugzilla.gromacs.org/issues/1306 > > The following parameters give a segfault in single precision but are ok in > double precision > sc-alpha = 0.001 > sc-power = 1 > sc-r-power = 48 > Same goes for http://bugzilla.gromacs.org/issues/1306 > > Sorry for the confusion earlier. I was using a compilation that I thought was > double precision > but it was actually single. Recompiling in double precision gave me the > stability outlined above. > > Thank you for your assitance Mark and Michael. > > Chris. > > -- original message -- > > Michael Shirts mrshirts at gmail.com > Fri Sep 27 00:41:17 CEST 2013 > Previous message: [gmx-users] segfault when running the alchemistry.org > ethanol solvation free energy tutorial > Next message: [gmx-users] segfault when running the alchemistry.org ethanol > solvation free energy tutorial > Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] > And with this change, single is running fine as well. > > This was a known issue, but was only documented in the expanded.mdp > files, which was an oversight. After this, I switched so the default > is less likely to cause problems. Because of some theory improvements > developed in the group in free energy calculation pathways, the > sc-r-power=48 pathway will now be phased out anyway by 5.1. > > On Thu, Sep 26, 2013 at 6:37 PM, Michael Shirts wrote: >> I thought I had just managed to solve the issue :) >> >> If you look at the soft core parameters, there are two types listed -- >> one with sc-r-power = 48, and one with sc-r-power = 6. The sc-r-power >> are more stable with single precision calculations. >> >> I have changed the files on the website to make the single precision >> ones the default. Expanded.mdp warned about the issues with >> precision, but left the sc-r-power in place; the Ethanol.mdp did not >> warn about the potential issue. Now both include the more efficient >> path commented out. >> >> NOTE that this means the exact numbers of the tutorials are not quite >> right anymore; the process is unchanged, as is the final answer, but >> the intermediate dG's will be slightly different. >> >> However, I need to redo them anyway to make them easier in the next >> 1-2 weeks, so I will update them then. >> >> If it still fails with double, that's a different issue -- because I'm >> running them fine with double. >> >> > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] "Illegal instruction" error from alchemical-gromacs.py
Dear Users: I'm having difficulty running MBAR after some free energy calculations (MBAR via alchemical-gromacs.py obtained from alchemistry.org). The input options to alchemical-gromacs.py have obviously changed since the site at http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy was updated, but I've taken a look at the python source and it seems as if my invocation below should work. Nevertheless, I get an "Illegal instruction" error (See below). gpc-logindm02-$ ls ANALYSIS/ ethanol.0.dhdl.xvg ethanol.2.dhdl.xvg ethanol.4.dhdl.xvg ethanol.6.dhdl.xvg ethanol.8.dhdl.xvg ethanol.1.dhdl.xvg ethanol.3.dhdl.xvg ethanol.5.dhdl.xvg ethanol.7.dhdl.xvg gpc-logindm02-$ python /project/p/pomes/cneale/GPC/exe/pymbar/trunk/examples/alchemical-free-energy/alchemical-gromacs.py -d ANALYSIS -p ethanol. -t 300 -s 1000 -v Warning on use of the timeseries module: If the inherent timescales of the system are long compared to those being analyzed, this statistical inefficiency may be an underestimate. The estimate presumes the use of many statistically independent samples. Tests should be performed to assess whether this condition is satisfied. Be cautious in the interpretation of the data. Started on Thu Sep 26 22:32:05 2013 Illegal instruction (omitting the -t -s and -v flags yields the same error). I realize that I'm hijacking the gromacs list a little bit here but there is no mailing list for http://www.alchemistry.org/ and it seems like a good idea to have these Q&A's archived. Thank you, Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Membrane simulation with OPLS ff.
Dear Karthi: As far as I am aware, there is no OPLSAA lipid force field. I have used Berger lipids with OPLSAA protein ( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is mixing a UA lipid with an AA protein so be aware of possible problems arising out of that. Charmm has proteins and lipids, but charmm lipids require charmm tip3p water (or at least tip4p or spc, certainly not regular tip3p) and are thus slower to simulate in gromacs. I'm more recently using the Slipids (stockholm lipids) and Amber99SB-ILDN protein forcefield. Chris. -- original message -- Is OPLSAA forcefield data already available for POPC membranes. I am interested in simulation of proteins in POPC membrane. Thank you. Best Regards Karthi. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Membrane simulation with OPLS ff.
On 9/26/13 10:47 PM, Christopher Neale wrote: Dear Karthi: As far as I am aware, there is no OPLSAA lipid force field. I have used Berger lipids with OPLSAA protein ( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is mixing a UA lipid with an AA protein so be aware of possible problems arising out of that. There are OPLS-compatible lipids, though they are UA, but specifically designed to be used with OPLS-AA: dx.doi.org/10.1021/ct900086b I have not seen these parameters used very widely, though. Charmm has proteins and lipids, but charmm lipids require charmm tip3p water (or at least tip4p or spc, certainly not regular tip3p) and are thus slower to simulate in gromacs. I'm more recently using the Slipids (stockholm lipids) and Amber99SB-ILDN protein forcefield. Solid choices. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] "Illegal instruction" error from alchemical-gromacs.py
Hi, Chris- The best place to file this issue is the SimTK pymbar page, rather than alchemistry.org, since it's a pymbar problem. We have collaborators that may have updated the pymbar.py recently. I'll try to get this stabilized in the very near future. Testing quickly, my best guess is that it's not alchemical-gromacs.py (latest version seems to work fine for me), but the pymbar installation that is causing problems. Give the illegal instruction calculations, the helper C++ code is probably causing a problem; perhaps it compiled using headers from the wrong version of numpy. In most cases, the best way is to explicitly force it to use the pure python. If you just delete the compiled _pymbar.so, then it will default to pure Python. It may be slower (5-10x) but it should still finish in a minute or two. I'm working on getting instructions for g_bar up there in alchemistry.org as well, but there are some bugs in g_bar that I am dealing with. On Thu, Sep 26, 2013 at 10:35 PM, Christopher Neale wrote: > Dear Users: > > I'm having difficulty running MBAR after some free energy calculations (MBAR > via alchemical-gromacs.py obtained from alchemistry.org). > The input options to alchemical-gromacs.py have obviously changed since the > site at > http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy > was updated, but I've taken a look at the python source and it seems as if my > invocation below should work. > Nevertheless, I get an "Illegal instruction" error (See below). > > gpc-logindm02-$ ls ANALYSIS/ > ethanol.0.dhdl.xvg ethanol.2.dhdl.xvg ethanol.4.dhdl.xvg > ethanol.6.dhdl.xvg ethanol.8.dhdl.xvg > ethanol.1.dhdl.xvg ethanol.3.dhdl.xvg ethanol.5.dhdl.xvg ethanol.7.dhdl.xvg > > gpc-logindm02-$ python > /project/p/pomes/cneale/GPC/exe/pymbar/trunk/examples/alchemical-free-energy/alchemical-gromacs.py > -d ANALYSIS -p ethanol. -t 300 -s 1000 -v > Warning on use of the timeseries module: If the inherent timescales of the > system are long compared to those being analyzed, this statistical > inefficiency may be an underestimate. The estimate presumes the use of many > statistically independent samples. Tests should be performed to assess > whether this condition is satisfied. Be cautious in the interpretation of > the data. > Started on Thu Sep 26 22:32:05 2013 > Illegal instruction > > (omitting the -t -s and -v flags yields the same error). > > I realize that I'm hijacking the gromacs list a little bit here but there is > no mailing list for http://www.alchemistry.org/ > and it seems like a good idea to have these Q&A's archived. > > Thank you, > Chris. > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] OPLS/AA + TIP5P, anybody?
Dear Gigo: I've never used tip5p, but perhaps you could add some LJ terms to the opls_120 definition, do your minimization, then remove the fake LJ term on opls_120 and run your MD? If that doesn't work, then you might be able to minimize your system using FLEXIBLE tip3p water and then use a script to convert the tip3p into tip5p. I expect that you can set 0,0,0 coordinates for each of the tip5p dummy atoms and that they will get correctly positioned in your first mdrun step with tip5p. Chris. -- original message -- Dear Mark, Thank you for your reply. Unfortunately, TIP5P is completely rigid and the FLEXIBLE define will not change it. Any other ideas? Best, g On 2013-09-24 23:51, Mark Abraham wrote: > You should be able to minimize with CG and TIP5P by eliminating > constraints, by making the water use a flexible molecule, e.g. define > = -DFLEXIBLE (or something). Check your water .itp file for how to do > it. > > Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Writing periodic image coordinates.
Thank you Sir! Regards Kavya On Fri, Sep 27, 2013 at 12:52 AM, Tsjerk Wassenaar wrote: > Hi Kavya, > > genconf -nbox 3 3 3 > > Cheers, > > Tsjerk > > > On Thu, Sep 26, 2013 at 6:24 PM, Kavyashree M wrote: > > > Dear users, > > > > For some analysis I require the 27 periodic images > > of the system I ran the simulation for. Kindly let me > > know how can it be written to a pdb file. > > > > Thanking you > > Regards > > Kavya > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat after trjconv
Thanks for the quick reply sir. So, does it mean I can apply "trjcat" on the processed xtc files??? On Thu, Sep 26, 2013 at 10:25 PM, Tsjerk Wassenaar wrote: > Hi Venkat, > > These options are 'frame intrinsic' or 'history independent', unlike -pbc > nojump. > > Cheers, > > Tsjerk > > On Sep 26, 2013 6:46 PM, "Venkat Reddy" wrote: > > Dear Tsjerk sir, > I used trjconv -pbc mol -ur compact options. > > On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar > wrote: > Hi Venkat, > > It... > > > -- > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/g... > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjcat after trjconv
Yes. Cheers, Tsjerk On Fri, Sep 27, 2013 at 7:51 AM, Venkat Reddy wrote: > Thanks for the quick reply sir. > So, does it mean I can apply "trjcat" on the processed xtc files??? > > > On Thu, Sep 26, 2013 at 10:25 PM, Tsjerk Wassenaar >wrote: > > > Hi Venkat, > > > > These options are 'frame intrinsic' or 'history independent', unlike -pbc > > nojump. > > > > Cheers, > > > > Tsjerk > > > > On Sep 26, 2013 6:46 PM, "Venkat Reddy" wrote: > > > > Dear Tsjerk sir, > > I used trjconv -pbc mol -ur compact options. > > > > On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk Wassenaar > > wrote: > Hi Venkat, > > It... > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/g... > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > With Best Wishes > Venkat Reddy Chirasani > PhD student > Laboratory of Computational Biophysics > Department of Biotechnology > IIT Madras > Chennai > INDIA-600036 > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
