[gmx-users] Tabulated non-bonded potentials - regd
Dear Gromacs users, In forcefield of my system, I have non-bonded function of the form U = A*exp(-Brij) - C/(rij^6) - D/(rij^4), for this I wanted to use tabulated potentials. I have defined functions f(r), g(r) and h(r) as the following, f = 1/r; fprime = 1/(pow(r,2)); g = (C*(-1/(pow(r,6; gprime = (-6*C/(pow(r,7))); h = A*exp(-B*r); hprime = ((A*B)*(exp(-B*r))); Then I have tabulated all these with a bin size (dr) of 0.002 nm and given nbfunc as 1 in forcefield.itp and provided C and A as 1 in ffnonbonded.itp (As I have used A,B C values in generation of table itself) . I have generated one such table for each interaction. While running simulations with these tables I am getting the following warning: WARNING: For the 3999 non-zero entries for table 2 in table.xvg the forces deviate on average 78% from minus the numerical derivative of the potential After this job is crashing with error Segmentation fault 1) Can anybody please tell me the reason for the above Warning and how one can rectify it ? 2) Can I define the functions for the above mentioned non-bonded function like this ? I have checked potential energy of model system (single point energy calculations i.e., zero step MD and the one that obtained from the code that I have written, both are matching. I am using GROMACS version 4.5.5 and also tested the same thing in V 4.6. Can anybody help me in this regard, Thank you in advance. Regards, Ramesh. -- 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] dummy atom - regd
Dear Bogdan, Thank you for reply. Best, Ramesh. On Mon, Feb 18, 2013 at 5:31 PM, Bogdan Costescu bcoste...@gmail.comwrote: On Mon, Feb 18, 2013 at 12:10 PM, Mark Abraham mark.j.abra...@gmail.com wrote: b) a particle needs to be at that immobile reference point - you can measure a distance to a point whether or not there is something there. I'm not sure that it's the same use-case... I recently talked to someone trying to define such a fixed particle to be used as a pull group. This pull group could then be set as reference in the middle of the PBC box, such that the pull distances are smaller than half the box size. The fact that the particle is really fixed when the PBC box is allowed to change dimensions is not a big problem, if needed the size of the box for each trajectory frame can then be used to correct distances. I don't know what was the outcome, but I'm curious to see such a setup. Cheers, Bogdan -- 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] Dummy/ghost atom - regd
Dear Gromacs users, I am planing to have a reference atom(non-bonded) in my system, whose position will not change during simulations and shouldn't feel/exert any force from/on the other atoms(ghost atom). How can I do this in gromacs ? can I set electrostatic and van der waals parameters to zero ? or is there any efficient way to do this ? Any help will be highly appreciated. Regards, Ramesh. -- 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] DD cells - regd
Dear Bogdan Costescu, Thank you for your valuable suggestion. Regards, Ramesh. On Mon, Jan 14, 2013 at 8:20 PM, Bogdan Costescu bcoste...@gmail.comwrote: On Sat, Jan 12, 2013 at 10:04 AM, ramesh cheerla rameshgrom...@gmail.com wrote: This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells This gives another possible solution. You decrease the number of DD grid cells by reducing the numbers of cores on which mdrun runs. Or, for the same number of cores, you can control better the decomposition using the '-dd' option in case the constraints are aligned to one of the 3 main directions. Cheers, Bogdan -- 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] DD cells - regd
Dear GROMACS users, After 20 ns production run, my simulation got crashed with the following error: Fatal error: DD cell 1 0 0 could only obtain 605 of the 606 atoms that are connected via constraints from the neighboring cells. This probably means your constraint lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs-order or use the -rcon option of mdrun. I have used the following options related to lincs in my .mdp file: lincs_iter = 1 lincs_order = 4 now I want to restart my simulation, by making use of the -rcon option with out disturbing lincs options as they are related to accuracy. Here my doubt is how I can I select value for the -rcon to restart my simulation ? or Is there any better option to get rid of this error ? Thank you in advance. Regards, Ramesh. -- 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] Umbrella sampling - regd
Dear Justin, Thank you very much for your quick reply. Regards, Ramesh. On Wed, Jan 2, 2013 at 10:24 AM, Justin Lemkul jalem...@vt.edu wrote: On 1/1/13 11:48 PM, ramesh cheerla wrote: Dear Gromacs users, I am performing umbrella sampling simulations by selecting configurations with spacing window of 0.02nm from pulling simulations with the following options in .mdp file to get PMF along a axis for permeation of ion through a channel. ; Pull code pull= umbrella pull_geometry = position ; simple distance increase pull_dim = N Y N pull_vec1= 0 -1 0 pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = FIXEDATOM pull_group1 = SMDATOM pull_rate1 = 0.0 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 2000 ; kJ mol^-1 nm^-2 pull_init1 = 0 And am using g_wham to get PMF, while using g_wham, am getting the warnings like : WARNING, no data point in bin 139 (z=-0.492557) ! You may not get a reasonable profile. Check your histograms! Warning, poor sampling bin 193 (z=-0.364322). Check your histograms! Warning, poor sampling bin 194 (z=-0.361947). Check your histograms! Warning, poor sampling bin 195 (z=-0.359572). Check your histograms! Warning, poor sampling bin 196 (z=-0.357197). Check your histograms! Warning, poor sampling bin 197 (z=-0.354823). Check your histograms! Warning, poor sampling bin 198 (z=-0.352448). Check your histograms! Warning, poor sampling bin 199 (z=-0.350073). Check your histograms! Initialized rapid wham stuff (contrib tolerance 6.7e-08) Evaluating only 2115 of 3000 expressions. I have checked my histograms and PMF profile, by doing so I have understood that histograms overlapping is restricted to only some regions and there is no histograms at all in some regions i.e severe sampling problems at barrier regions. here I am sending the link that containing PMF profile that I have obtained, http://researchweb.iiit.ac.in/** ~bipin.singh/pmf.jpg http://researchweb.iiit.ac.in/~bipin.singh/pmf.jpg Can anybody tell me how can I get proper sampling at barrier regions is there any efficient way to do this, how about meta dynamics with suitable CV (collective variable) ? . Use a stronger force constant in these barrier regions to restrict the movement along the reaction coordinate. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] Umbrella sampling - regd
Dear Justin, I am very thankful to you for your reply, you are correct, I have plotted the histo.xvg file in wrong manner. After plotting histograms in correct manner I have realized that my sampling is very poor as histograms and there overlapping is restricted to some regions only, no histograms in some areas along reaction co-ordinate. I am not sure whether this lack of sampling is due to inappropriate selection of pulled configurations or inappropriate pull geometry. However I will try as per your suggestion and get back to you. Thank you, Regards, Ramesh. On Mon, Nov 26, 2012 at 7:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/26/12 1:03 AM, ramesh cheerla wrote: Dear Gromacs users, I am calculating PMF for the ion permeation through a tunnel, using umbrella sampling. In my system I have some binding sites with ions, I have removed some ions from binding sites before pulling and In pulling simulations have pullaed pulled the adjacent ions to the vacant binding site (tunnel is aligned along Y- axis). for this I have used the following options in .mdp file. ; Pull code pull= umbrella pull_geometry = distance pull_dim= N Y N pull_start = yes pull_ngroups= 1 pull_group0 = REFA pull_rate1 = 0.01 pull_k1 = 3000 ; kJ mol^-1 nm^-2 Here pull_group0 = REFA is the ion at another binding site and pull_group1 = ATBP is the atom that I am pulling to the vacant site. In next step I have performed umbrella sampling simulations to the selected configurations using the following options : ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N Y N pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = REFA pull_group1 = ATBP pull_init1 = 0 pull_rate1 = 0.0 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 3000 ; kJ mol^-1 nm^-2 pull_nstxout= 100 pull_nstfout= 100 After that I have constructed PMF profile using Gromacs tool g_wham, while using g_wham I am getting the following warnings, WARNING, no data point in bin 34 (z=0.889382) ! You may not get a reasonable profile. Check your histograms! I have checked my histograms instead of one histogram for each configuration with perfect overlapping, I am getting only one histogram. You're probably just plotting the file wrong. xmgrace -nxy histo.xvg Here I am sending the link that containing PMF profile and histogram that have obtained. http://researchweb.iiit.ac.in/**~bipin.singh/pmf.jpghttp://researchweb.iiit.ac.in/~bipin.singh/pmf.jpg http://researchweb.iiit.ac.in/**~bipin.singh/hist.jpghttp://researchweb.iiit.ac.in/~bipin.singh/hist.jpg The PMF suggests massive undersampling (or complete lack of sampling) in several areas. the weired thing that I have observed in my pulling simulations is that I have expected motion of ion in positive Y-direction for my pull parameters but it is moving in negative Y- direction. Can anybody please suggest me a solution for this, Am I following correct protocol to get PMF of my system, is there any better method that suits for my system. If you are trying to see a complete translocation of an ion through a channel, the distance geometry is inappropriate, as it does not deal correctly with the change of sign for the vector between the reference and pulled group, IIRC. Try position geometry and associated settings. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] rapid change in the angle of simulation cell - regd
Dear Tsjerk, Thank you for your valuable suggestions, I have done as you have suggested, by doing so my simulation cell has satisfied all the conditions required for the reduced basis lattice but now lattice parameter beta has again changed to 102 degrees which was initially taken as 125.4 degrees as provided by crystallographers. Is there a way so that I can continue my simulations in Gromacs with the lattice parameters provided by crystallographers as I am intending to measure how lattice parameters vary with temperature and compare them with the experimental results. Now, I am unable to compare my lattice parameters with experimental values as Gromacs is changing the simulation cell to its convenient way (beta starting from 102 degrees originally should be 125.4 degrees ). Thank you in advance, Regards, Ramesh. On Wed, Oct 10, 2012 at 4:51 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Ramesh, You already got a good handle on it! You can subtract and add vectors without changing the lattice. Now, the box in gromacs will be something like ((ax, 0, 0), (bx,by,0),(cx,cy,cz)). If cx 0.5*ax, then you can change the vector to (cx-ax,cy-0,cz-0), and the new |cx'| will always be smaller than ax. Cheers, Tsjerk On Wed, Oct 10, 2012 at 11:47 AM, ramesh cheerla rameshgrom...@gmail.com wrote: Dear Tsjerk, I am very thankful to you for your reply and sorry for delay as it has taken much time to understand the things properly. I have gone through the material that you have attached with this mail that is really useful. Now I have understood that large change in beta value of my simulation cell is because of Gromacs's convenient way to choose the periodic boundary conditions and not because of forcefield that I have used. From your mail and Gromacs manual I have understood that, the box vectors of a simulation unit cell should satisfy the three conditions given in the chapter-3 of manual( eqs:3.1,3.2 3.3) if simulation unit cell satisfies these conditions then that is called the reduced basis lattice(am i correct ? ). According to you if we start the simulations with reduced basis lattice then the difference in the angles of reference system and the simulated system will become lesser. For my simulations I have generated simulation cell by using editconf as : editconf -f input.gro -bt triclinic-box 3.30 2.7 8.055 -angles 90 125.4 90 -o output_box.gro then I have extracted box vectors from the output.gro and checked for the validity of condition given in the chapter-3 of manual, from this I understood that the generated box obeying all the conditions except the one in 3.3 i.e |Cx| =1/2ax . Here my doubt is what changes can I make to my system in order to make it follow all the rules required for the reduced basis lattice without disturbing its morphology as it is a crystal, that means how can I rotate, orient or align my system are there any built in tools in GROMACS to achieve this and how would I get new box vectors and angles after rotating/aligning to generate the box for modified system. Thank you in advance. Regards, Ramesh. On Thu, Sep 27, 2012 at 1:09 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Ramesh, Did you note how your atoms didn't change their positions? And how you can still stack them using either set of vectors? It's a great example of how PBC works. It's not the box that's important, not the vectors, but the infinite simulation system that results from stacking the unit cell contents, using the lattice vectors. And there's an infinite number of lattice vectors that give the same result. Not all of these vectors are practical to work with from a computational point of view. What Gromacs does is choosing the vectors that are most convenient to work with, which is laid down in the rules for box vectors given in chapter 3 of the manual. This is called the reduced basis of the lattice. For what you want to do, you need to identify the smallest difference angle between the lattice vectors in your system and your reference. The best way to do that is to work with the reduced basis from the start. Any other set of lattice vectors will give lower difference angles. If you don't really get what I'm writing here, you may want to check Appendix A in http://dissertations.ub.rug.nl/FILES/faculties/science/2006/t.a.wassenaar/03_c3.pdf Hope it helps, Tsjerk On Wed, Sep 26, 2012 at 7:32 AM, ramesh cheerla rameshgrom...@gmail.com wrote: Dear Gromacs users, I am performing simulations of a polymer crystal in Gromacs, for these simulations I have generated a triclinic box, and have done one step minimization. In the single step minimization itself the simulation box angle beta is varying from 125.4 degrees to 102
Re: [gmx-users] rapid change in the angle of simulation cell - regd
Dear Tsjerk, I am very thankful to you for your reply and sorry for delay as it has taken much time to understand the things properly. I have gone through the material that you have attached with this mail that is really useful. Now I have understood that large change in beta value of my simulation cell is because of Gromacs's convenient way to choose the periodic boundary conditions and not because of forcefield that I have used. From your mail and Gromacs manual I have understood that, the box vectors of a simulation unit cell should satisfy the three conditions given in the chapter-3 of manual( eqs:3.1,3.2 3.3) if simulation unit cell satisfies these conditions then that is called the reduced basis lattice(am i correct ? ). According to you if we start the simulations with reduced basis lattice then the difference in the angles of reference system and the simulated system will become lesser. For my simulations I have generated simulation cell by using editconf as : editconf -f input.gro -bt triclinic-box 3.30 2.7 8.055 -angles 90 125.4 90 -o output_box.gro then I have extracted box vectors from the output.gro and checked for the validity of condition given in the chapter-3 of manual, from this I understood that the generated box obeying all the conditions except the one in 3.3 i.e |Cx| =1/2ax . Here my doubt is what changes can I make to my system in order to make it follow all the rules required for the reduced basis lattice without disturbing its morphology as it is a crystal, that means how can I rotate, orient or align my system are there any built in tools in GROMACS to achieve this and how would I get new box vectors and angles after rotating/aligning to generate the box for modified system. Thank you in advance. Regards, Ramesh. On Thu, Sep 27, 2012 at 1:09 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Ramesh, Did you note how your atoms didn't change their positions? And how you can still stack them using either set of vectors? It's a great example of how PBC works. It's not the box that's important, not the vectors, but the infinite simulation system that results from stacking the unit cell contents, using the lattice vectors. And there's an infinite number of lattice vectors that give the same result. Not all of these vectors are practical to work with from a computational point of view. What Gromacs does is choosing the vectors that are most convenient to work with, which is laid down in the rules for box vectors given in chapter 3 of the manual. This is called the reduced basis of the lattice. For what you want to do, you need to identify the smallest difference angle between the lattice vectors in your system and your reference. The best way to do that is to work with the reduced basis from the start. Any other set of lattice vectors will give lower difference angles. If you don't really get what I'm writing here, you may want to check Appendix A in http://dissertations.ub.rug.nl/FILES/faculties/science/2006/t.a.wassenaar/03_c3.pdf Hope it helps, Tsjerk On Wed, Sep 26, 2012 at 7:32 AM, ramesh cheerla rameshgrom...@gmail.com wrote: Dear Gromacs users, I am performing simulations of a polymer crystal in Gromacs, for these simulations I have generated a triclinic box, and have done one step minimization. In the single step minimization itself the simulation box angle beta is varying from 125.4 degrees to 102 degrees. Decrement of beta value by 23.4 degrees in single step might not be acceptable. what is the way to seize this large change in beta value ? Here I am sending link to the picture of my system with simulation cell before and after minimization of one step(1fs). http://researchweb.iiit.ac.in/~bipin.singh/new.png Can anybody please go through the image and provide the reasonable solution, as the angle variations of the simulation cell are one of important analyses in my studies. Thank you in advance, Regards, Ramesh. -- 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. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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
[gmx-users] Decoupling non-bonded energies - regd
Dear Gromacs user, I want to decouple non-bonded energies of some of the pairs of atoms from total non-bonded energy, how can I do this in gromacs. Anybody can suggest me a away to do this ? Thank you in advance . Regards, Ramesh. -- 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] Variation of angles of simulation cell - regd
Dear Mark, Thank you very much for your reply, I will change options in .mdp file accordingly to get deformations in all possible directions. Thank you. On Mon, Sep 10, 2012 at 9:41 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 10/09/2012 1:52 PM, ramesh cheerla wrote: Dear Mark, Thank you very much for your reply and valuable suggestions, I have used compressibility values as compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0 in my .mdp file. So you're getting the (lack of) box deformations you're asking for with these zero compressibilities. Having non-zero off-diagonal compressibilities with ref_p sounds like a disaster, too. Actually I am interested in melting simulations of a polymer crystal, but I haven't found any compressibility values for my system in literature, So that I have used compressibility values of water in my simulations, Can I do like this ?. Maybe. You need to do some literature work, not ask some semi-random people on the internet :-). Mark Following is the my .mdp file used for production, can you please go through the .mdp file and suggest me if any modifications are required to get correct lattice parameters. title = CHARMM 27 MD ; Run parameters integrator = md; leap-frog integrator nsteps = 50; 2 * 50 = 1000 ps, 1 ns dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = system; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 20; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = anisotropic ; non uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 1.0 1.0 0.0 0.0 0.0 ; reference pressure, in bar compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off Thank you in advance. On Sun, Sep 9, 2012 at 9:17 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 9/09/2012 11:41 PM, ramesh cheerla wrote: Dear Gromacs users, Recently I have converted each frame of the trajectory to a pdb file using gromacs tool g_trjconv and then have extracted angles from the CRYST1 record of pdb file, to see how they are varying in simulation. By doing so I have observed that my box angles alpha and gamma are not at all varying through out the simulation these values are remains at 90 degrees and there is a change in beta value. I have used triclinic box for simulations of my system with angles alpha = 90, beta=120 and gamma=90 and have used NPT ensemble with following options in mdp file pcoupltype = anisotropic and ref_p = 1.0 1.0 1.0 0.0 0.0 0.0 here my questions are: 1) What might be the probable reason for constant values of alpha and beta ( why these values are not changing). See 7.3.15, which of course you read before using anisotropic coupling. You're making life hard by not giving your full .mdp file, because you're leaving us to guess about your compressibilities. Do summarise, but don't exclude. :-) Presumably your choices are consistent with a monoclinic box staying that way. 2
[gmx-users] Rotational time correlation function - regd
Dear Gromacs users, I want to calculate rotational correlation function for my system, parallel to Z- axis and perpendicular to Z-axis(lateral), -- 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] Rotational correlation function - regd
Dear Gromacs users, I am interested in calculating rotational correlation function for my system, parallel to Z- axis and perpendicular to Z-axis(lateral), how can I do this by using gromacs tool g_rotacf. As the g_rotacf has the option to calculate total rotation correlation function, how can I split this into correlation along a particular axis and perpendicular to the same axis ? Any help will be highly appreciated. Thank you, Regards, Ramesh. -- 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] Variation of angles of simulation cell - regd
Dear Gromacs users, Recently I have converted each frame of the trajectory to a pdb file using gromacs tool g_trjconv and then have extracted angles from the CRYST1 record of pdb file, to see how they are varying in simulation. By doing so I have observed that my box angles alpha and gamma are not at all varying through out the simulation these values are remains at 90 degrees and there is a change in beta value. I have used triclinic box for simulations of my system with angles alpha = 90, beta=120 and gamma=90 and have used NPT ensemble with following options in mdp file pcoupltype = anisotropic and ref_p = 1.0 1.0 1.0 0.0 0.0 0.0 here my questions are: 1) What might be the probable reason for constant values of alpha and beta ( why these values are not changing). 2) Am I following correct protocol to extract angles, or Is there any better way to extract angles from trajectory. 3) Am I using correct options in .mdp file. Thank you in advance. Regards, Ramesh. -- 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] Variation of angles of simulation cell - regd
Dear Mark, Thank you very much for your reply and valuable suggestions, I have used compressibility values as compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0 in my .mdp file. Actually I am interested in melting simulations of a polymer crystal, but I haven't found any compressibility values for my system in literature, So that I have used compressibility values of water in my simulations, Can I do like this ?. Following is the my .mdp file used for production, can you please go through the .mdp file and suggest me if any modifications are required to get correct lattice parameters. title = CHARMM 27 MD ; Run parameters integrator = md; leap-frog integrator nsteps = 50; 2 * 50 = 1000 ps, 1 ns dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; Bond parameters continuation= yes ; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = system; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 20; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = anisotropic ; non uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 1.0 1.0 0.0 0.0 0.0 ; reference pressure, in bar compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off Thank you in advance. On Sun, Sep 9, 2012 at 9:17 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 9/09/2012 11:41 PM, ramesh cheerla wrote: Dear Gromacs users, Recently I have converted each frame of the trajectory to a pdb file using gromacs tool g_trjconv and then have extracted angles from the CRYST1 record of pdb file, to see how they are varying in simulation. By doing so I have observed that my box angles alpha and gamma are not at all varying through out the simulation these values are remains at 90 degrees and there is a change in beta value. I have used triclinic box for simulations of my system with angles alpha = 90, beta=120 and gamma=90 and have used NPT ensemble with following options in mdp file pcoupltype = anisotropic and ref_p = 1.0 1.0 1.0 0.0 0.0 0.0 here my questions are: 1) What might be the probable reason for constant values of alpha and beta ( why these values are not changing). See 7.3.15, which of course you read before using anisotropic coupling. You're making life hard by not giving your full .mdp file, because you're leaving us to guess about your compressibilities. Do summarise, but don't exclude. :-) Presumably your choices are consistent with a monoclinic box staying that way. 2) Am I following correct protocol to extract angles, or Is there any better way to extract angles from trajectory. If you want lattice parameters, that's probably the best way to get them. 3) Am I using correct options in .mdp file. Can't tell. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx
Re: [gmx-users] Variation of box angles - regd
Hi Tsjerk, I am very thankful to you for providing valuable suggestions. Thank you very much. On Tue, Aug 28, 2012 at 9:23 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Ramesh, You can calculate them from the box matrix, or you can let editconf do that by simply converting the trajectory (or a small part thereof) to PDB format. The angles are then in the CRYST1 record. Cheers, Tsjerk On Aug 27, 2012 2:15 PM, ramesh cheerla rameshgrom...@gmail.com wrote: Dear GMX users, I want to see how box angles are varying during my simulations, I have no idea where box angles will be stored in gromacs output files and how to extract them . Can anybody please help me in this regard. Thank you in advance Regards, Ramesh. -- 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] Variation of box angles - regd
Dear GMX users, I want to see how box angles are varying during my simulations, I have no idea where box angles will be stored in gromacs output files and how to extract them . Can anybody please help me in this regard. Thank you in advance Regards, Ramesh. -- 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] box vectors - regd
Dear Mark, Once again I am very thankful to you for your reply, I have extracted box vectors from .XTC file by using g_traj with -ob option with this I was able to get only six vector components viz XX YY ZZ YX ZX and ZY only how about remaining three vector components XY XZ and YZ . I have used triclinic box for my simulations I know that XY XZ and YZ will be zero, moreover I have used pcoupltype = anisotropic with compressibility values as compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0 in my .mdp file. Here my question is why I am not getting XY XZ and YZ components in my output file though they might be zero. Is this because of above specified .mdp options or something else ? Can you please let me know what might be the probable reason ? Thank you in advance. On Thu, Aug 16, 2012 at 11:17 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/08/2012 3:22 PM, ramesh cheerla wrote: Dear Mark, Thank you for your reply, as you suggested I will go through the sec 7.4 and 8 of the manual and moreover how would I get exact box vectors XX YY ZZ XY XZ YX YZ ZX ZY for each frame of trajectory in gromacs They're in the trajectory file with each frame. As I am new to gromacs I have no Idea where these will be stored ( other than gro file ). In NAMD .XTC file contains box vectors for each step of the simulation like this is there any file in gromacs that stores these box vectors for each step, Same. if so how can i extract them. Probably however you did so with NAMD, or with g_traj or gmxdump. Mark Please suggest me a way. Thank you. On Thu, Aug 16, 2012 at 4:52 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/08/2012 5:46 AM, ramesh cheerla wrote: Dear Gromacs users, I am using gromacs for simulations of a polymer, for that I am planing to see how lattice parameters a , b c are varying during simulation. Here lattice parameter a is the length of unit cell along X- direction, b is the length of the unit cell along Y axis and c is along Z -axis. For my polymer polymer chains are not exactly oriented along Z- direction they are a little bit tilted from the Z- axis. a and b are along x and Y directions respectively so that I can get lattice parameters a and b just by dividing box lengths along those directions with the number of unit cells in those directions. As the c- direction and Z- direction are not exactly same ( c is a little bit tilted from Z ) in this case I shouldn't divide the box length along Z - direction with the number of unit cells in that direction to get lattice parameter c. Here my questions are: 1) How can I calculate exact C lattice parameter from simulation data ? is there any way to get appropriate c? 2) How one can get box vectors XX YY ZZ XY XZ YX YZ ZX and ZY for total trajectory, as g_energy is giving only Box - X , Box-Y and Box- Z but i need exact box vectors for valid lattice parameters calculations. Sounds like g_energy is reminding you that you had a rectilinear simulation cell when you started, and still do. There are various ways to measure angles that will help you address your problem, if you check out manual sections 7.4 and 8. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] box vectors - regd
Dear Gromacs users, I am using gromacs for simulations of a polymer, for that I am planing to see how lattice parameters a , b c are varying during simulation. Here lattice parameter a is the length of unit cell along X- direction, b is the length of the unit cell along Y axis and c is along Z -axis. For my polymer polymer chains are not exactly oriented along Z- direction they are a little bit tilted from the Z- axis. a and b are along x and Y directions respectively so that I can get lattice parameters a and b just by dividing box lengths along those directions with the number of unit cells in those directions. As the c- direction and Z- direction are not exactly same ( c is a little bit tilted from Z ) in this case I shouldn't divide the box length along Z - direction with the number of unit cells in that direction to get lattice parameter c. Here my questions are: 1) How can I calculate exact C lattice parameter from simulation data ? is there any way to get appropriate c? 2) How one can get box vectors XX YY ZZ XY XZ YX YZ ZX and ZY for total trajectory, as g_energy is giving only Box - X , Box-Y and Box- Z but i need exact box vectors for valid lattice parameters calculations. Any help will be highly appreciated. Thank you in advance. Regards, Ramesh. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] box vectors - regd
Dear Mark, Thank you for your reply, as you suggested I will go through the sec 7.4 and 8 of the manual and moreover how would I get exact box vectors XX YY ZZ XY XZ YX YZ ZX ZY for each frame of trajectory in gromacs As I am new to gromacs I have no Idea where these will be stored ( other than gro file ). In NAMD .XTC file contains box vectors for each step of the simulation like this is there any file in gromacs that stores these box vectors for each step, if so how can i extract them. Please suggest me a way. Thank you. On Thu, Aug 16, 2012 at 4:52 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 16/08/2012 5:46 AM, ramesh cheerla wrote: Dear Gromacs users, I am using gromacs for simulations of a polymer, for that I am planing to see how lattice parameters a , b c are varying during simulation. Here lattice parameter a is the length of unit cell along X- direction, b is the length of the unit cell along Y axis and c is along Z -axis. For my polymer polymer chains are not exactly oriented along Z- direction they are a little bit tilted from the Z- axis. a and b are along x and Y directions respectively so that I can get lattice parameters a and b just by dividing box lengths along those directions with the number of unit cells in those directions. As the c- direction and Z- direction are not exactly same ( c is a little bit tilted from Z ) in this case I shouldn't divide the box length along Z - direction with the number of unit cells in that direction to get lattice parameter c. Here my questions are: 1) How can I calculate exact C lattice parameter from simulation data ? is there any way to get appropriate c? 2) How one can get box vectors XX YY ZZ XY XZ YX YZ ZX and ZY for total trajectory, as g_energy is giving only Box - X , Box-Y and Box- Z but i need exact box vectors for valid lattice parameters calculations. Sounds like g_energy is reminding you that you had a rectilinear simulation cell when you started, and still do. There are various ways to measure angles that will help you address your problem, if you check out manual sections 7.4 and 8. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] Isothermal compressibility for polymers - regd
Dear GMX users, How one can calculate Isothermal compressibility for given system ( eg : Materials like polymers ) using gromacs. Thank you in advance. Regards, Ramesh Cheerla. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Checking interaction energies - regd
Dear Gromacs users, I am using buckingham potential in my simulations for that I have copied charmm27.ff to my working directory, and have modified it, to know whether it is working properly or not, I have run one step simulations and checked the energies obtained in simulations with the energies obtained in the programs that I have written to calculate these energies, In this case non-bonded and dihedral energies are matching perfectly, and am getting a difference of bond stretching energy 1.74 Kj/mol per bond and a large variation in bending energies i.e 56.4 kj/mol per angle, for bending i have used function type 1 and included same functional form i.e 0.5*Ktheta*(theta-theta0)^2 in my program and I have used all the units according to Gromacs conventions in my programs. Can anyone please explain the reason for difference. Thank you in advance. Regards, Ramesh. -- 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] user specified non bonded potentials - regd
Dear Gromacs users, I am planning to use tabulated potentials for the non-bonded interactions for my system. As my system contain some non-bonded interactions in the standard buckingham format and some interactions are similar to buckingham ( i.e., buckingham + some polarization term). Here my doubt is can we use the tables only for the interactions which contain buckingham + polarization term and remaining interactions through standard buckingham potential ( without tables ) ? i.e., Is it possible to use both tables and normal standard interactions together in gromacs ? I have understood that atomic interactions specified in energygrp_tables read potentials from specific tables and atomic interactions which are specified in energygrps and not specified in energygrp_table will read potentials from general table table.xvg. here my doubt is how about the atomic interactions which are not specified in energygrps and energygrp_tables. Do they read potentials from the general table table.xvg or not . Can we use normal potentials to these interactions alone without tables. Any help will be highly appreciated. Thank you in advance. Regards, Ramesh. -- 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] Tabulated potentials for dihedrals - regd
Dear Mark, I am very Thankful to you for your valuable suggestion. On Thu, Jun 7, 2012 at 12:04 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 7/06/2012 4:33 AM, ramesh cheerla wrote: Dear Mark, Thank you for your reply, According to my understanding functional form of dihedral function type 9 is same as dihedral function type 1 i.e k (1 + cos(n (phi)- phi s)) except the difference that function type 9 is used to handle the multiple potential functions to be applied to the single dihedreal, Is my understanding correct ?. The functional form that I am using Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 is different from the k (1 + cos(n (phi)- phi s)). I am suspecting can I use function type 9 for my function. Can you please clarify my doubt. I said last time you can use type 9. You can use high-school maths to express your equation in the form of a sum of multiple type 1, which is type 9. The additive constant only affects the total energy, which is never used for the simulation. The derivative of V is used, so the constant goes away. Mark Thank you in advance. On Mon, Jun 4, 2012 at 12:55 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/06/2012 3:46 AM, ramesh cheerla wrote: Dear Gromacs experts, I am planing to use tabulated potentials for dihedral functional form Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 . I have three different K values (i.e K1,K2,K3 ) one for each 'n' value ( Here 'n' is multiplicity). You do not need a table for this - type 9 will do the job easily, and for friendly values of phi0, there exists an equivalent form to the above that can be expressed as a Ryckaert-Belleman dihedral. See various places of manual chapters 4 and 5. I have generated table and given the table number in dihedrals directive of the ffbonded.itp file, According to my understanding one has to supply K ( force constant ) value in addition to table number in topology. In my case I have three different K values, which k value do I have to take, Can I take sum of all the three k values or can I take arbitrary value. Your table would need to be the weighted sum of the three cosines, so apparently you have not yet generated such a table. But rather than buy trouble, go and do the easier and faster solutions above :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Tabulated potentials for dihedrals - regd
Dear Mark, Thank you for your reply, According to my understanding functional form of dihedral function type 9 is same as dihedral function type 1 i.e k (1 + cos(n (phi)- phi s)) except the difference that function type 9 is used to handle the multiple potential functions to be applied to the single dihedreal, Is my understanding correct ?. The functional form that I am using Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 is different from the k (1 + cos(n (phi)- phi s)). I am suspecting can I use function type 9 for my function. Can you please clarify my doubt. Thank you in advance. On Mon, Jun 4, 2012 at 12:55 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 4/06/2012 3:46 AM, ramesh cheerla wrote: Dear Gromacs experts, I am planing to use tabulated potentials for dihedral functional form Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 . I have three different K values (i.e K1,K2,K3 ) one for each 'n' value ( Here 'n' is multiplicity). You do not need a table for this - type 9 will do the job easily, and for friendly values of phi0, there exists an equivalent form to the above that can be expressed as a Ryckaert-Belleman dihedral. See various places of manual chapters 4 and 5. I have generated table and given the table number in dihedrals directive of the ffbonded.itp file, According to my understanding one has to supply K ( force constant ) value in addition to table number in topology. In my case I have three different K values, which k value do I have to take, Can I take sum of all the three k values or can I take arbitrary value. Your table would need to be the weighted sum of the three cosines, so apparently you have not yet generated such a table. But rather than buy trouble, go and do the easier and faster solutions above :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-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] Tabulated potentials for dihedrals - regd
Dear Gromacs experts, I am planing to use tabulated potentials for dihedral functional form Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 . I have three different K values (i.e K1,K2,K3 ) one for each 'n' value ( Here 'n' is multiplicity). I have generated table and given the table number in dihedrals directive of the ffbonded.itp file, According to my understanding one has to supply K ( force constant ) value in addition to table number in topology. In my case I have three different K values, which k value do I have to take, Can I take sum of all the three k values or can I take arbitrary value. Any help please. Thank you in advance. Regards, Ramesh. -- 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] Polarization term in non-boded potential - Regd
Hi all, I am planing to use Gromacs for the simulation of my system, for which the non-bonded interaction potential has the polarization term as -Dij/(rij**4) in addition to the Bucking ham potential and electrostatic interactions. So the non-bonded potential will appear as U(r)NB = A exp( -rij B) - C/rij**6 - D/rij**4 + qiqj/rij Here the units for the polarization term is nm^4 Kcal/mol How can I handle this kind of potentials in gromacs ? Can I use tabulated potential for this ? Please help me in this regard, Thank you in advance. Regards, Ramesh Cheerla. -- 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] tabulated potentials for dihedrals - regd
Dear Gromacs users, I am using tabulated potentials for the dihedrals of my system, the dihedral function I am using is Summn over 'n' 0.5*K [ ( Cos n(phi-phi0)] , Here 1= n = 3 . The C-O-C-C dihedral of my system has three folds those are n= 1 , 2, 3 and three different K ( force constant ) values one for each n value. Here my doubt is while specifying the k value in the ffbonded.itp , Which K value do I have to take ? or can i take sum of all these k values and mention that value in ffbonded.itp ? Please help me in this regard, Thank you in advance, Regards, Ramesh cheerla. -- 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] Tabulated potentials for the Dihedrals - regd
Dear Gromacs users, I am using tabulated potentials for dihedrals of my system which is of form dih = (1/2)*K[COS n(phi-phi0)], Here n=3. I have generated table_d0.xvg by uniformly varying phi as 0.1 from -180 to 180 and calculated the numerical derivative and force by using the relations der = Y(n+1)- Y(n-1)/ (2*h) ; force = -der ; Here h = step size (i.e 0.1 in my case). Here I have some doubts: 1) Am I using the correct relations for calculation of derivative and force. 2) which value should we take for the k ( force constant) in ffbonded.itp, the value of k that specified with the dihedral potential ? or some arbitrary number ? As I have used the value of k given with the dihedral function in calculations of potential and the force, Is it necessary to mention force constant value again in ffbonded.itp and 3) if I run mdrun as mdrun -tableb table_do.xvg it giving the error : Library file table_d0_d0.xvg not found in current dir nor in default directories. Can you please suggest me the correct way of using the -tableb option in the case of multiple tables. Thank you in advance, Regards, Ramesh Cheerla. -- 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] Wild-card atomt types - regd
Dear Gromacs users, I am planing to use wildcard atomtypes in [ dihedrals ] directive of the ffbonded.itp file, As my system contain O-C dihedral, all the O-C dihedrals are same, so instead of mentioning each dihedral explicitly i have tried wildcard atom types by specifing X-O-C-X but couldn't succeed,It is giving the error: No default Proper Dih. types. Is there any specific method to use wildcard atom types in Gromacs for dihedrals or do I have to define the wildcard atomtypes, if so in which file do i have to define it. Any help will be highly appreciated. Thank you in advance. Best regards, Ramesh cheerla -- 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] Wildcard atomtypes-regd
Dear Gromacs users, I am planing to use wildcard atomtypes in [ dihedrals ] directive of the ffbonded.itp file, As my system contain O-C dihedral, all the O-C dihedrals are same, so instead of mentioning each dihedral explicitly i have tried wildcard atom types by specifing X-O-C-X but couldn't succeed,It is giving the error: No default Proper Dih. types. Is there any specific method to use wildcard atom types in Gromacs for dihedrals or do I have to define the wildcard atomtypes, if so in which file do i have to define it. Any help will be highly appreciated. Thank you in advance. Regards, Ramesh Cheerla. -- 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] multiple dihedral function types - regd
Dear gromacs users, For one of my residues i have two types of dihedral functions, i.e C-C dihedrals are in periodic type and C-O dihedrals are in the Ryckaert-bellemans type, now i want to generate the topology file for this residue is it possible to use the two dihedral function types for this residue. I have tried by using two different dihedraltypes directives one is for the periodic type and another one is for Ryckaert-Bellemans function, but how can i incorporate the two functional types in the dihedrals section of the bondedtypes directive in aminoacids.rtp. or is there any methods in gromacs to convert one dihedral functional form to the other. Thank you, Regards, Ramesh. -- 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] Box generation for monoclinic crystal - regd
Dear Mark, Thank you for reply, sorry for not being very clear, Here my doubt is can i use triclinic box for the simulations of the crystal whose unit cell is monoclinic. As i said earlier i have tried editconf as editconf -f input.gro -o out_box1.gro -bt triclinic -box 3.22 2.608 7.792 -angles 90 125.4 90 it gave the following warning WARNING: Triclinic box is too skewed. for clarity here i am sending a part of the output file generated by the editconf God Rules Over Mankind, Animals, Cosmos and Such 6528 1PEGAC11 -0.025 0.408 -0.045 1PEGAC22 -0.015 0.326 0.084 ; 3.22000 2.60800 6.35148 0.0 0.0 0.0 0.0 -4.51376 -0.0 if i change the angles while using the editconf i observed the following changes editconf -f input.gro -o out_box2.gro -bt triclinic -box 3.22 2.608 7.792 -angles 90 90 125.4 in this case editconf haven't given any warning and the output as follows God Rules Over Mankind, Animals, Cosmos and Such 6528 1PEGAC11 1.477 0.167 0.675 1PEGAC22 1.487 0.085 0.804 ; 3.22000 2.12585 7.79200 0.0 0.0 -1.51077 0.0 -0.0 -0.0 Can you please help me in this regard. thank you in advance. On Mon, Ap;r 9, 2012 at 11:55 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/04/2012 3:22 PM, ramesh cheerla wrote: Dear Gromacs users, I am planing to simulate a polymeric crystal in gromacs, which is of monoclinic unit cell with cell parameters a = 0.805 nm b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of 424 type i.e 4 unit cells along 'a' direction '2' unit cells along 'b' direction and 4 unit cells along 'c' direction. So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm. I am using editconf to generate box for this crystal as: editconf -f input.gro -o out_box.gro -bt tric -box 3.22 2.608 7.792 -angles 90 125.4 90 Here i have some doubts: 1) Am i using the editconf in correct manner for generation of box for the monoclinic crystal, though the crystal is of monoclinic i am using box type as triclinic i haven't found any specific method for the generation of box for the monoclinic crystal. 2) Is there any specific method to generate the box for the monoclinic crystals. 3) The notations for the lattice parameters of the crystal i.e 'a' , 'b' , 'c' and angles alpha, beta , gamma used by crystallography and the gromacs editconf are the same or different, why because if i use editconf as above i am getting the following warning: WARNING: Triclinic box is too skewed. This means equation 3.3 of the manual is not true. Maybe beta should be acute? I've no idea of necessity or convention here. Inspecting the whole output of editconf is probably instructive, but you've kept all that information to yourself instead of re-thinking how your repeat post might be constructed so as to make it easier / more likely for people help you. Likewise the final line of out_box.gro. Make sure you have read and understood what documentation is available with editconf -h and in manual section 3.2. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-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] Box generation for monoclinic crystal - regd
Dear Tsjerk, Thank you for your reply, I will try to work with PDB format and get back to you. On Wed, Apr 11, 2012 at 12:22 AM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Ramesh, Maybe it is easier, and less error-prone, to work in PDB format, specifying the box as a CRYST1 record. You can use the PDB format anywhere in your workflow where GRO format is used. Cheers, Tsjerk On Tue, Apr 10, 2012 at 8:13 PM, ramesh cheerla rameshgrom...@gmail.com wrote: Dear Mark, Thank you for reply, sorry for not being very clear, Here my doubt is can i use triclinic box for the simulations of the crystal whose unit cell is monoclinic. As i said earlier i have tried editconf as editconf -f input.gro -o out_box1.gro -bt triclinic -box 3.22 2.608 7.792 -angles 90 125.4 90 it gave the following warning WARNING: Triclinic box is too skewed. for clarity here i am sending a part of the output file generated by the editconf God Rules Over Mankind, Animals, Cosmos and Such 6528 1PEGAC11 -0.025 0.408 -0.045 1PEGAC22 -0.015 0.326 0.084 ; 3.22000 2.60800 6.35148 0.0 0.0 0.0 0.0 -4.51376 -0.0 if i change the angles while using the editconf i observed the following changes editconf -f input.gro -o out_box2.gro -bt triclinic -box 3.22 2.608 7.792 -angles 90 90 125.4 in this case editconf haven't given any warning and the output as follows God Rules Over Mankind, Animals, Cosmos and Such 6528 1PEGAC11 1.477 0.167 0.675 1PEGAC22 1.487 0.085 0.804 ; 3.22000 2.12585 7.79200 0.0 0.0 -1.51077 0.0 -0.0 -0.0 Can you please help me in this regard. thank you in advance. On Mon, Ap;r 9, 2012 at 11:55 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 9/04/2012 3:22 PM, ramesh cheerla wrote: Dear Gromacs users, I am planing to simulate a polymeric crystal in gromacs, which is of monoclinic unit cell with cell parameters a = 0.805 nm b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of 424 type i.e 4 unit cells along 'a' direction '2' unit cells along 'b' direction and 4 unit cells along 'c' direction. So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm. I am using editconf to generate box for this crystal as: editconf -f input.gro -o out_box.gro -bt tric -box 3.22 2.608 7.792 -angles 90 125.4 90 Here i have some doubts: 1) Am i using the editconf in correct manner for generation of box for the monoclinic crystal, though the crystal is of monoclinic i am using box type as triclinic i haven't found any specific method for the generation of box for the monoclinic crystal. 2) Is there any specific method to generate the box for the monoclinic crystals. 3) The notations for the lattice parameters of the crystal i.e 'a' , 'b' , 'c' and angles alpha, beta , gamma used by crystallography and the gromacs editconf are the same or different, why because if i use editconf as above i am getting the following warning: WARNING: Triclinic box is too skewed. This means equation 3.3 of the manual is not true. Maybe beta should be acute? I've no idea of necessity or convention here. Inspecting the whole output of editconf is probably instructive, but you've kept all that information to yourself instead of re-thinking how your repeat post might be constructed so as to make it easier / more likely for people help you. Likewise the final line of out_box.gro. Make sure you have read and understood what documentation is available with editconf -h and in manual section 3.2. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx
Re: [gmx-users] multiple dihedral function types - regd
Thank you mark. On Wed, Apr 11, 2012 at 8:09 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 11/04/2012 3:33 AM, ramesh cheerla wrote: Dear gromacs users, For one of my residues i have two types of dihedral functions, i.e C-C dihedrals are in periodic type and C-O dihedrals are in the Ryckaert-bellemans type, now i want to generate the topology file for this residue is it possible to use the two dihedral function types for this residue. I have tried by using two different dihedraltypes directives one is for the periodic type and another one is for Ryckaert-Bellemans function, but how can i incorporate the two functional types in the dihedrals section of the bondedtypes directive in aminoacids.rtp. You can't. That is a limitation of pdb2gmx. or is there any methods in gromacs to convert one dihedral functional form to the other. Basic trig will let you express a periodic dihedral of sufficiently small periodicity in R-B form. However that's only a reasonable solution with pdb2gmx if the force field uses only R-B dihedrals. It may be more effective to use pdb2gmx and to replace the inappropriate dihedral form in the .top file by hand afterwards. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-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] Box generation for monoclinic crystal - regd
Thank you mark. On Wed, Apr 11, 2012 at 6:15 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 11/04/2012 4:13 AM, ramesh cheerla wrote: Dear Mark, Thank you for reply, sorry for not being very clear, Here my doubt is can i use triclinic box for the simulations of the crystal whose unit cell is monoclinic. As i said earlier i have tried editconf as editconf -f input.gro -o out_box1.gro -bt triclinic -box 3.22 2.608 7.792 -angles 90 125.4 90 it gave the following warning WARNING: Triclinic box is too skewed. for clarity here i am sending a part of the output file generated by the editconf God Rules Over Mankind, Animals, Cosmos and Such 6528 1PEGAC11 -0.025 0.408 -0.045 1PEGAC22 -0.015 0.326 0.084 ; 3.22000 2.60800 6.35148 0.0 0.0 0.0 0.0 -4.51376 -0.0 if i change the angles while using the editconf i observed the following changes editconf -f input.gro -o out_box2.gro -bt triclinic -box 3.22 2.608 7.792 -angles 90 90 125.4 Isn't that a totally different box? See editconf -h about -angles. Mark in this case editconf haven't given any warning and the output as follows God Rules Over Mankind, Animals, Cosmos and Such 6528 1PEGAC11 1.477 0.167 0.675 1PEGAC22 1.487 0.085 0.804 ; 3.22000 2.12585 7.79200 0.0 0.0 -1.51077 0.0 -0.0 -0.0 Can you please help me in this regard. thank you in advance. On Mon, Ap;r 9, 2012 at 11:55 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 9/04/2012 3:22 PM, ramesh cheerla wrote: Dear Gromacs users, I am planing to simulate a polymeric crystal in gromacs, which is of monoclinic unit cell with cell parameters a = 0.805 nm b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of 424 type i.e 4 unit cells along 'a' direction '2' unit cells along 'b' direction and 4 unit cells along 'c' direction. So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm. I am using editconf to generate box for this crystal as: editconf -f input.gro -o out_box.gro -bt tric -box 3.22 2.608 7.792 -angles 90 125.4 90 Here i have some doubts: 1) Am i using the editconf in correct manner for generation of box for the monoclinic crystal, though the crystal is of monoclinic i am using box type as triclinic i haven't found any specific method for the generation of box for the monoclinic crystal. 2) Is there any specific method to generate the box for the monoclinic crystals. 3) The notations for the lattice parameters of the crystal i.e 'a' , 'b' , 'c' and angles alpha, beta , gamma used by crystallography and the gromacs editconf are the same or different, why because if i use editconf as above i am getting the following warning: WARNING: Triclinic box is too skewed. This means equation 3.3 of the manual is not true. Maybe beta should be acute? I've no idea of necessity or convention here. Inspecting the whole output of editconf is probably instructive, but you've kept all that information to yourself instead of re-thinking how your repeat post might be constructed so as to make it easier / more likely for people help you. Likewise the final line of out_box.gro. Make sure you have read and understood what documentation is available with editconf -h and in manual section 3.2. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Box generation for monoclinic crystal - regd
Dear Gromacs users, I am planing to simulate a polymeric crystal in gromacs, which is of monoclinic unit cell with cell parameters a = 0.805 nm b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of 424 type i.e 4 unit cells along 'a' direction '2' unit cells along 'b' direction and 4 unit cells along 'c' direction. So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm. I am using editconf to generate box for this crystal as: editconf -f input.gro -o out_box.gro -bt tric -box 3.22 2.608 7.792 -angles 90 125.4 90 Here i have some doubts: 1) Am i using the editconf in correct manner for generation of box for the monoclinic crystal, though the crystal is of monoclinic i am using box type as triclinic i haven't found any specific method for the generation of box for the monoclinic crystal. 2) Is there any specific method to generate the box for the monoclinic crystals. 3) The notations for the lattice parameters of the crystal i.e 'a' , 'b' , 'c' and angles alpha, beta , gamma used by crystallography and the gromacs editconf are the same or different, why because if i use editconf as above i am getting the following warning: WARNING: Triclinic box is too skewed. Thank you in advance, Regards, Ramesh. -- 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] Polymer crystal simulations-regd
Dear Gromacs users, I am trying to simulate a polymer crystal in gromacs, which is of monoclinic unit cell with cell parameters a = 0.805 nm, b = 1.304 nm, c = 1.948 nm, beta = 125.4 deg. my crystal consists of 4 unit cells along 'a' , 2 unit cells along 'b' and 4 unit cells along 'c' , So lengths of my box vectors are a = 3.22 nm, b = 2.608, c = 7.792 and beta = 125.4 For defining box for the simulations of my crystal i am using editconf as editconf -f input.gro -o out_box.gro -bt tric -box 3.22 2.608 7.792 -angles 90 125.4 90 Am not sure whether am I using the correct format or not ? Is there any specific method to mention the monoclinic cell for the simulations in gromacs.? If i use like this i am getting the following warning: WARNING: Triclinic box is too skewed. Any help will be highly appreciated. Regards, Ramesh. -- 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] Monoclinic crystal simulations- gromacs - Regd
Dear Gromacs users, I am planing to simulate a polymeric crystal in gromacs, which is of monoclinic unit cell with cell parameters a = 0.805 nm b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of 424 type i.e 4 unit cells along 'a' direction '2' unit cells along 'b' direction and 4 unit cells along 'c' direction. So my box vector lengths are a = 3.22 nm, b = 2.608 nm, c = 7.792 nm. I am using editconf to generate box for this crystal as: editconf -f input.gro -o out_box.gro -bt tric -box 3.22 2.608 7.792 -angles 90 125.4 90 Here i have some doubts: 1) Am i using the editconf in correct manner by mentioning box type as triclinic though the crystal is of monoclinic 2) Is there any specific method to generate the box for the monoclinic crystals. 3) The notations for the lattice parameters of the crystal i.e 'a' , 'b' , 'c' and angles alpha, beta , gamma used by crystallography and the gromacs editconf are the same or different, why because if i use editconf as above i am getting the following warning: WARNING: Triclinic box is too skewed. Thank you in advance, Regards, Ramesh. -- 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] Options for the buckingham potential
Thank you for your valuble suggestion. On Fri, Feb 24, 2012 at 12:02 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 24/02/2012 5:15 PM, Mark Abraham wrote: On 24/02/2012 4:06 PM, ramesh cheerla wrote: Dear Gromacs users, i am planning to use buckingham potential for non-bonded interactions. i am specifying the same thing in the [defaults] directive of the forcefield.itp file as [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 2 1 no0.0 1.0 Here my doubt are 1) Am i using correct options for the combination-rule and fudgeQQ ? See 4.1.2 for combination rule. Actually, 4.1.2 is wrong about the combination rule for B. See example in 5.7.1 for correct combination rule. Mark fudgeQQ effects electrostatic interactions. 2) what i understood from manual is usage of option 'yes' for the gen-pairs is not allowed with the buckingham potential and fudgeLj is used only when gen-pairs is set to 'yes' is my understanding correct? Yes. See 5.7.1 Mark Thank you in advance. Regards, Ramesh. -- 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] Adding new residue to the the force field
Dear Mark, Thanks for your reply. I am not using both LJ and Buckingham in the same simulation, but trying to use only Buckingham . As my system is a polymer which is made of the monomer unit that's what i am adding to the force field. Our polymer system uses the parameters only from the residue which i have added to the forcefield through buckingham A,B C parameters. I would like to ask the previous question again, Which values can i use for the [ pairtypes ] directive in the ffnonbonded.itp can i use arbitrary values or zeroes what i noticed from my simulations is by changing the sigma and epsilon values in the [ pairtypes ] directive energy values are changing. if i try to comment out the pairtypes 'grompp' is generating the following errors( here i am sending only one error message ) ERROR 411 [file topol.top, line 862]: No default LJ-14 types i am a little bit confused why grompp is giving this error message though i am using the bucking potential by specifying the nbfunc as 2 in the [ default ] directive and providing the A,B,C values through [nonbond_params ] . if it is mandatory to use pair types how can i get these values for this directive. Thanks in advance. On Fri, Feb 24, 2012 at 12:15 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 24/02/2012 5:20 PM, ramesh cheerla wrote: Dear Mark I am very thank ful to you for your valuble suggestion. I have verified my results by changing the sigma and epsilon values in [atomtypes ] directive of the ffnonbonded.itp . Results were uneffected by changing these values. Here i have one another doubt regarding [ pairtypes ] directive, As I am using buckingham potential for the nonbonded interactions and have only A, B C values can i use zeros for the sigma and epsilon values in this directive. What i observed is results will change by changing the sigma and epsilon values in this directive. Please suggest me how can i use correct values for the sigma and epsilon in [ pairtypes ] directive. As I understand things, pairs for special 1-4 interactions are not used with Buckingham interactions. Looking closer at your original post, you claim to be adding a residue using Buckingham to an existing force field. No force fields distributed with GROMACS use Buckingham, so if you're trying to make both LJ and Buckingham work in the same simulation, you will be unable to succeed. Mark Thank you in advance. On Thu, Feb 23, 2012 at 7:32 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 23/02/2012 6:02 AM, ramesh cheerla wrote: Dear gromacs users, I am adding a new residue to the existing force field in gromacs for that i am using some new atom types i added these atom types to the atomtypes.atp file and ffnonbonded.itp and I am using Buckingham potential for the non-bonded interactions for that i have only A,BC values, but in the [atomtype] directive of the ffnonbonded.itp file one has to specify the sigma and epsilon values. How can i get these values ? or can i specify these values as zeros ? You will be able to use zeroes. You can verify that there's no effect by changing the values to ludicrous ones and observing that the simulation is the same. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Options to be specified for the buckingham potential
Dear Gromacs users, i am planning to use buckingham potential for non-bonded interactions. i am specifying the same thing in the [defaults] directive of the forcefield.itp file as [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 2 1 no0.0 1.0 Here my doubt are 1) Am i using correct options for the combination-rule and fudgeQQ ? 2) what i understood from manual is usage of option 'yes' for the gen-pairs is not allowed with the buckingham potential and fudgeLj is used only when gen-pairs is set to 'yes' is my understanding correct? Thank you in advance. Regards, Ramesh. -- 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] Options for the buckingham potential
Dear Gromacs users, i am planning to use buckingham potential for non-bonded interactions. i am specifying the same thing in the [defaults] directive of the forcefield.itp file as [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 2 1 no0.0 1.0 Here my doubt are 1) Am i using correct options for the combination-rule and fudgeQQ ? 2) what i understood from manual is usage of option 'yes' for the gen-pairs is not allowed with the buckingham potential and fudgeLj is used only when gen-pairs is set to 'yes' is my understanding correct? Thank you in advance. Regards, Ramesh. -- 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] Adding new residue to the the force field
Dear Mark I am very thank ful to you for your valuble suggestion. I have verified my results by changing the sigma and epsilon values in [atomtypes ] directive of the ffnonbonded.itp . Results were uneffected by changing these values. Here i have one another doubt regarding [ pairtypes ] directive, As I am using buckingham potential for the nonbonded interactions and have only A, B C values can i use zeros for the sigma and epsilon values in this directive. What i observed is results will change by changing the sigma and epsilon values in this directive. Please suggest me how can i use correct values for the sigma and epsilon in [ pairtypes ] directive. Thank you in advance. On Thu, Feb 23, 2012 at 7:32 AM, Mark Abraham mark.abra...@anu.edu.auwrote: On 23/02/2012 6:02 AM, ramesh cheerla wrote: Dear gromacs users, I am adding a new residue to the existing force field in gromacs for that i am using some new atom types i added these atom types to the atomtypes.atp file and ffnonbonded.itp and I am using Buckingham potential for the non-bonded interactions for that i have only A,BC values, but in the [atomtype] directive of the ffnonbonded.itp file one has to specify the sigma and epsilon values. How can i get these values ? or can i specify these values as zeros ? You will be able to use zeroes. You can verify that there's no effect by changing the values to ludicrous ones and observing that the simulation is the same. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-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] Adding new residue to the the force field
Dear gromacs users, I am adding a new residue to the existing force field in gromacs for that i am using some new atom types i added these atom types to the atomtypes.atp file and ffnonbonded.itp and I am using Buckingham potential for the non-bonded interactions for that i have only A,BC values, but in the [atomtype] directive of the ffnonbonded.itp file one has to specify the sigma and epsilon values. How can i get these values ? or can i specify these values as zeros ? Any help will be highly appreciated Thank you Regards, Ramesh -- 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] modifications required for the ffnonbonded.itp while adding a new residue
Dear Gromacs users, i am adding new residue to the existing charmm27 force field of the gromacs and i am planning to use buckingham potential for the non bonded interactions. for that i made following changes to the ffnonbonded.itp file [ atomtypes ] ;name at.num masscharge ptype sigma epsilon CC32A 6 12.01100 0.1030 A 0.0 0.00.0 HCA21 1.00800 0.0355 A 0.0 0.00.0 OC30A 8 15.999400 -0.3480 A 0.0 0.00.0 [ pairtypes ] ; i j funcsigma1-4epsilon1-4 ; THESE ARE 1-4 INTERACTIONS OC30A OC30A 1 0.0 0.0 OC30A CC32A 1 0.0 0.0 OC30A HCA2 1 0.0 0.0 CC32A CC32A10.0 0.0 CC32A HCA2 10.0 0.0 HCA2HCA2 10.0 0.0 ;### I have given the A(in KJ/mol), B(in nm^-1), C(in Kj/mol*nm^6) [ nonbond_params ] ; i j funcsigma1-4epsilon1-4 ; THESE ARE 1-4 INTERACTIONS OC30A OC30A2 243922.597640.2414486921 0.000803746 OC30A CC32A2 179625.814436.297640653 0.001476115 OC30A HCA2 2 85489.9984 40.899795501 0.000413379 CC32A CC32A2 132277.578433.057851240.002710395 CC32A HCA2 2 62955.3928 36.832412523 0.000759396 HCA2HCA2 2 29962.4608 41.580041580.000212547 ;### I have given the A(in KJ/mol), B(in nm^-1), C(in Kj/mol*nm^6) ;D = A, B = 1/P, C = E and in the default directive of the forcefield.itp i made the following changes [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 2 1 no 0.0 0.0 what values should i give for the sigma and epsilon in the [ atomtype ] directive and pairtypes directive . if i ignore the pair types it giving error no default Lj 1-4 interactions. though i am using nbfun as 2 to use the buckingham potential. I have only the values of the A,B,C. How to get sigma and epsilon if they are required. Did i modify the ffnonbonded.itp in the correct manner ? or any thing went wrong? please help me in this regard. Thank you in advance. Regards, Ramesh. -- 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] How to use Buckingham potentials ?
Dear Gromacs users, I am planing to use buckingham potential for the non-bonded interactions of my system. I know that by changing the nbfunc to 2 in [ defaults ] directive of topology will allow to use the Buckingham potential , But I don't know how to specify the A, B,C values in the ffnonbonded.itp file. what values should I specify in the [ atomtypes ] directive . As i know only A,B,C values for the pairs of atoms so i have tried by specifying A,B,C values both in [ atomtypes ] and [ pairtypes ] as [ atomtypes ] ;name at.num mass chargeptype A B C CC32A 6 12.011000.1030A 132277.5784 33.057851240.002710395 HCA2 1 1.00800 0.0355 A 29962.4608 41.580041580.000212547 OC30A 8 15.999400 -0.3480 A 243922.5976 40.2414486921 0.000803746 [ pairtypes ] ; i j func A BC OC30A OC30A 2 243922.597640.2414486921 0.000803746 OC30A CC32A 2 179625.814436.297640653 0.001476115 OC30A HCA22 85489.9984 40.899795501 0.000413379 CC32A CC32A 2 132277.578433.057851240.002710395 CC32A HCA22 62955.3928 36.832412523 0.000759396 HCA2HCA22 29962.4608 41.580041580.000212547 ;### I have given the A(in KJ/mol), B(in nm^-1), C(in Kj/mol*nm^6) ;D = A, B = 1/P, C = E Doing so , grompp is showing the following errors ERROR 5 [file ffnonbondedpeo.itp, line 13]: Too many parameters or not enough parameters for topology B ERROR 6 [file ffnonbondedpeo.itp, line 14]: Too many parameters or not enough parameters for topology B Generated 6 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'polymer' ERROR 7 [file topol.top, line 1652]: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. -- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 1372 Fatal error: There were 7 errors in input file --- Any help will be highly appreciated. Regards, Ramesh Cheerla -- 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] How to assign charge group codes to atoms of new residue -Regd
Dear Gromacs users, As i am planning to use Gromacs for simulations of my system consisting of CH3-CH2-O, and as the CH3-CH2-O residue parameters are not available by default in charmm27.ff, so i am trying to add the parmeters of this residue to charmm27.ff,but struck where i am not sure how to assign charge group codes which will be denoting the charge group numbers for the atoms of this residue in .rtp file.Is there any procedure that has to be followed to assign particular values as charge group codes. Any help will be highly appreciated. Thank you Regards, Ramesh -- 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
