[gmx-users] Re: About the parameters for REMD in vacuum
Dear Ozge, lets keep the discussion in the gmx-users list. Thank you for your quick reply! I used the temperature distribution that was used in your paper: starting from 275.6 to 399.6. This distribution was chosen to give an exchange ratio of ~0.3 on the system used: a beta-peptide in methanol. Given that you change the system and thus the degrees of freedom you have adapt your temperatures. Their distribution has to be chosen such that the overlap of total potential energy of the system at consecutive temperatures allows exchange. You can tune the separations between the temperatures to vary the exchange rate. I used the 0.002 ps as time step, but I could not understand what you suggested exactly. You asked the time step for temperature coupling? Is is true? if so, the temperature coupling constant was 0.1. I was referring to the integration time step, which is the time step you use to integrate the equation of motion that are used to propagate your system in time. If you go to higher temperature the thermal energy is such that the motions of the atoms are increased and you need to decrease the time step of integration to be able to describe the evolution of the system. That might be the reason you see LINCS warnings. Then the fact that you do not use explicit solvent (no viscosity) will increase the motion of the particles (atoms) and may add to the problem described above. What temperature coupling constant and temperature interval will be appropriate for simulation in vacuum via REMD? delta=0.001 ps might be enough. You need to make some trials. But again, simulating in vacuo is almost useless, unless you want to show that the sampling is inaccurate. Have you ever performed REMD in vacuum? Yes to show that you get erroneous sampling. This is well accepted also there are few papers showing it explicitly. Same thing for the use of implicit solvents but this is more documented in the literature. Look for papers of AE. Garcia and co-workers. Ozge XAvier - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Chains blowing Apart
Hi All, I have been trying run energy minimization for a homoTRIMER protein, I have puzzled by the following results! 1) energy minimization in vacuum 1 chain is separated from the remaining 2 chains. I tried for 5 models in 4 models chains are separated and one is normal. 2)energy minimization in box with or with out solvent, no chain separation for all the 5 models. please note that EM method is steepest decent, I have tried size on the box up to 20nm. CONTESTS OF MDP FILE cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no What would be the probable reason for this. Please let me know. Regards Chandu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Chains blowing Apart
On Mon, 26 Nov 2007 13:45:01 +0530 (IST) [EMAIL PROTECTED] wrote: Hi All, I have been trying run energy minimization for a homoTRIMER protein, I have puzzled by the following results! 1) energy minimization in vacuum 1 chain is separated from the remaining 2 chains. I tried for 5 models in 4 models chains are separated and one is normal. 2)energy minimization in box with or with out solvent, no chain separation for all the 5 models. please note that EM method is steepest decent, I have tried size on the box up to 20nm. you are probably experiencing the effect of PBC. In the cases you see separation, centering the protein in the box should solve the problem. CONTESTS OF MDP FILE cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 100 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no What would be the probable reason for this. Please let me know. Regards Chandu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Chain separation problem
On Mon, 26 Nov 2007 15:33:36 +0530 (IST) [EMAIL PROTECTED] wrote: Dear Periole, Thank you so much for your suggestion. I was not sure weather to reply all or individually. It is always better to keep the discussion on the users list. The info given might serve other users. I am sorry I am not clear about your answer. I am getting the problem only when I am not using the box, but you said to center the protein in the box? Could you please explain this. When you use a box the program will deal with the position of the system relative to the box faces. If a molecule (first atom) moves and crosses the dimension of the box on one axis (x,y,z) -it physically gets out of the box- it will be replaced inside the box on the opposite box-side (same axis). Have a look at the manual or any text book on simulations, this will be more clearly explained. When you build your system, it might be that one part of it is inside the box and the other part is outside. This is more likely to happen when multimeric structures are simulated. Then the program will automatically replace the parts of the system that are outside the box to the inside. Note that the system does not feel it. If you want to avoid this you have to center your system before doing any minimization. Note that the box has to be large enough to accommodate your system plus solvent. XAvier Thanks in advance Chandu On Mon, 26 Nov 2007 13:45:01 +0530 (IST) [EMAIL PROTECTED] wrote: Hi All, I have been trying run energy minimization for a homoTRIMER protein, I have puzzled by the following results! 1) energy minimization in vacuum 1 chain is separated from the remaining 2 chains. I tried for 5 models in 4 models chains are separated and one is normal. 2)energy minimization in box with or with out solvent, no chain separation for all the 5 models. please note that EM method is steepest decent, I have tried size on the box up to 20nm. you are probably experiencing the effect of PBC. In the cases you see separation, centering the protein in the box should solve the problem. -- C.Chandra Sekhar Reddy (Research Scholar) Laboratoire de Biochimie et Génétique Moléculaire Université de La Réunion 15, avenue René Cassin 97715 Saint Denis Messag Cedex 09 La Réunion, France Tel : +262 262 93 8641 MOB +262 (0)692 44 49 42 Fax : +262 262 93 8237 -- - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Chain separation problem
On Mon, 26 Nov 2007 11:44:22 +0100 Xavier Periole [EMAIL PROTECTED] wrote: On Mon, 26 Nov 2007 15:33:36 +0530 (IST) [EMAIL PROTECTED] wrote: Dear Periole, Thank you so much for your suggestion. I was not sure weather to reply all or individually. It is always better to keep the discussion on the users list. The info given might serve other users. I am sorry I am not clear about your answer. I am getting the problem only when I am not using the box, but you said to center the protein in the box? Could you please explain this. Sorry I thought you had the problem only when using a box! Then I am also confused. Without boundaries this should not happen. Check you input must be something funny there. XAvier When you use a box the program will deal with the position of the system relative to the box faces. If a molecule (first atom) moves and crosses the dimension of the box on one axis (x,y,z) -it physically gets out of the box- it will be replaced inside the box on the opposite box-side (same axis). Have a look at the manual or any text book on simulations, this will be more clearly explained. When you build your system, it might be that one part of it is inside the box and the other part is outside. This is more likely to happen when multimeric structures are simulated. Then the program will automatically replace the parts of the system that are outside the box to the inside. Note that the system does not feel it. If you want to avoid this you have to center your system before doing any minimization. Note that the box has to be large enough to accommodate your system plus solvent. XAvier Thanks in advance Chandu On Mon, 26 Nov 2007 13:45:01 +0530 (IST) [EMAIL PROTECTED] wrote: Hi All, I have been trying run energy minimization for a homoTRIMER protein, I have puzzled by the following results! 1) energy minimization in vacuum 1 chain is separated from the remaining 2 chains. I tried for 5 models in 4 models chains are separated and one is normal. 2)energy minimization in box with or with out solvent, no chain separation for all the 5 models. please note that EM method is steepest decent, I have tried size on the box up to 20nm. you are probably experiencing the effect of PBC. In the cases you see separation, centering the protein in the box should solve the problem. -- C.Chandra Sekhar Reddy (Research Scholar) Laboratoire de Biochimie et Génétique Moléculaire Université de La Réunion 15, avenue René Cassin 97715 Saint Denis Messag Cedex 09 La Réunion, France Tel : +262 262 93 8641 MOB +262 (0)692 44 49 42 Fax : +262 262 93 8237 -- - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] [Fwd: Semiisotropic pressure coupling comm_grps (VCM)]
Original Message Subject:Semiisotropic pressure coupling comm_grps (VCM) Date: Mon, 26 Nov 2007 13:04:05 +0530 From: Alok [EMAIL PROTECTED] To: [EMAIL PROTECTED] Dear Sir, Sorry for personnel mail. I have posted these question in gromacs mailing list but I haven't got the answer. So I am sending you personally. I have two basic questions regarding membrane protein simulation. First regarding Semiisotropic pressure coupling (NPAT) and second regarding comm_grpp (VCM). 1) If I want to use NPAT ensemble (x/y dimensions of bilayer to be fixed) then is following the correct way to define? Pcoupl = Berendsen Pcoupltype= semiisotropic tau_p = 2.0 2.0 compressibility = 04.5e-5 ref_p = 1.0 1.0 In some of the previous mails on same topic ref_p was defined as 0.0 1.0 in place of 1.0 1.0 even they was using compressibility 0.0 4.5e-5, that's why I am confuse. Do I have to take ref_p = 1.0 1.0 or 0.0 1.0 when I am using compressibility 0.0 4.5e-5 (NPAT). I think if I am taking compressibility value 0 then it doesn't matter what value I have taken for ref_p, but I want to confirm it. 2) I want to remove center of mass translation so in following which one is better? a)comm_mode= Linear nstcomm = 1 comm_grps = Protein_POP ; (both protein and lipid are together) b)comm_mode= Linear nstcomm = 1 comm_grps = Protein POP ; (protein and lipid separately) Thanks a lot Best Regards, Alok -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Chain separation problem
Dear Periole, Thank you so much for your kind reply, as you suggested I will keep the discussion on the users list. Please note that I AM GETTING PROBLEM ONLY WHEN I AM NOT USING ANY BOX. When I am keeping the protein in the box with or with out solution chains are not separating. What I understood from your suggestion is solution for the chain separation in the box. Regards Chandu On Mon, 26 Nov 2007 15:33:36 +0530 (IST) [EMAIL PROTECTED] wrote: Dear Periole, Thank you so much for your suggestion. I was not sure weather to reply all or individually. It is always better to keep the discussion on the users list. The info given might serve other users. I am sorry I am not clear about your answer. I am getting the problem only when I am not using the box, but you said to center the protein in the box? Could you please explain this. When you use a box the program will deal with the position of the system relative to the box faces. If a molecule (first atom) moves and crosses the dimension of the box on one axis (x,y,z) -it physically gets out of the box- it will be replaced inside the box on the opposite box-side (same axis). Have a look at the manual or any text book on simulations, this will be more clearly explained. When you build your system, it might be that one part of it is inside the box and the other part is outside. This is more likely to happen when multimeric structures are simulated. Then the program will automatically replace the parts of the system that are outside the box to the inside. Note that the system does not feel it. If you want to avoid this you have to center your system before doing any minimization. Note that the box has to be large enough to accommodate your system plus solvent. XAvier Thanks in advance Chandu On Mon, 26 Nov 2007 13:45:01 +0530 (IST) [EMAIL PROTECTED] wrote: Hi All, I have been trying run energy minimization for a homoTRIMER protein, I have puzzled by the following results! 1) energy minimization in vacuum 1 chain is separated from the remaining 2 chains. I tried for 5 models in 4 models chains are separated and one is normal. 2)energy minimization in box with or with out solvent, no chain separation for all the 5 models. please note that EM method is steepest decent, I have tried size on the box up to 20nm. you are probably experiencing the effect of PBC. In the cases you see separation, centering the protein in the box should solve the problem. -- C.Chandra Sekhar Reddy (Research Scholar) Laboratoire de Biochimie et Génétique Moléculaire Université de La Réunion 15, avenue René Cassin 97715 Saint Denis Messag Cedex 09 La Réunion, France Tel : +262 262 93 8641 MOB +262 (0)692 44 49 42 Fax : +262 262 93 8237 -- - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - -- C.Chandra Sekhar Reddy (Research Scholar) Laboratoire de Biochimie et Génétique Moléculaire Université de La Réunion 15, avenue René Cassin 97715 Saint Denis Messag Cedex 09 La Réunion, France Tel : +262 262 93 8641 MOB +262 (0)692 44 49 42 Fax : +262 262 93 8237 -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] [Fwd: Semiisotropic pressure coupling comm_grps (VCM)]
I have two basic questions regarding membrane protein simulation. First regarding Semiisotropic pressure coupling (NPAT) and second regarding comm_grpp (VCM). 1) If I want to use NPAT ensemble (x/y dimensions of bilayer to be fixed) then is following the correct way to define? Pcoupl = Berendsen Pcoupltype= semiisotropic tau_p = 2.0 2.0 compressibility = 04.5e-5 ref_p = 1.0 1.0 In some of the previous mails on same topic ref_p was defined as 0.0 1.0 in place of 1.0 1.0 even they was using compressibility 0.0 4.5e-5, that's why I am confuse. Do I have to take ref_p = 1.0 1.0 or 0.0 1.0 when I am using compressibility 0.0 4.5e-5 (NPAT). I think if I am taking compressibility value 0 then it doesn't matter what value I have taken for ref_p, but I want to confirm it. I would guess that ref_p = 1.0 1.0 and ref_p = 0.0 1.0 would give the result since you define compressibility = 0.0 4.5e-05 you can check that by running small trajectories ... 2) I want to remove center of mass translation so in following which one is better? a)comm_mode= Linear nstcomm = 1 comm_grps = Protein_POP ; (both protein and lipid are together) b)comm_mode= Linear nstcomm = 1 comm_grps = Protein POP ; (protein and lipid separately) It is better to remove the COM of both bilayer (plus protein) and the aqueous phase: comm_grps = Protein_POP SOL XAvier Thanks a lot Best Regards, Alok -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Chain separation problem
Dear Periole, Thank you so much for your kind reply, as you suggested I will keep the discussion on the users list. Please note that I AM GETTING PROBLEM ONLY WHEN I AM NOT USING ANY BOX. Please also refrain from using all-capitals. It is regarded as the email equivalent of shouting. It will get your email ignored, rather than treated with more urgency. If your proteins-are-moving apart problem is not a PBC artifact, and does not occur when you use PBC, then you have a perplexing problem. First, check your inputs again, so that you really are doing what you think you're doing. Even repeat the whole setup from scratch. The simplest explanation is user error. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Confusion Regarding Vacuum
Dear All, I am a bit confused regarding Vacuum. I wanted to do EM in Vacuum. I think I can proceed either of the below... 1) I create a box (editconf) and place a molecule with out solvent. 2) Never create a box, then proceed other steps as usual like EM etc. Can we call 2nd option also a vacuum and what is more appropriate? Regards Chandu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Coarse-graining and tabulated non-bonded potentials - will write up on the wiki
Hello all, Firstly, many thanks to everyone who has contributed useful advice to me over a number of years using GROMACS. I have performed a large number of potential of mean force calculations for the forces acting between two approximately spherical amorphous silica particles (various sizes 5 nm diameter) in TIP4P water with PME electrostatics and varying concentrations of background ions. Now I want to 'coarse-grain' the simulation, treating each silica particle as a single point mass, and use the interaction potential between the particles obtained from the PMF results as a tabulated potential in mdrun, to allow longer time- and size-scales to be investigated (I want to examine colloidal aggregation behaviour of these particles). I have tabulated the PMF potential and its derivatives as a function of centre-of-mass separation of the particles as suggested in the manual (but I can only tabulate for COM-COM distances greater than the contact distance [ = 2r in the hard-sphere approximation] out to some cutoff). Will I have to add a short-distance 'hard-sphere' wall to my tabulated potentials? I have read the appropriate section of the manual on tabulated interactions, and am working on building an appropriate topology. IU am assuming that my coarse-grained particles consist of the silica particles plus a number of surface counterions in such a way that the particles will be electrically neutral, so presumably I can set all the entries in the tabulated potential file for the Coulomb terms to zero. If my understanding of the manual is correct, I can then introduce my PMF potential in one or other of the g() and h() columns, along with its appropriate derivatives. The plan is to randomly place a number of the coarse-grained particles in a simulation box and choose an appropriate time step and thermostat to run aggregation simulations. Some of the literature I have read suggests timesteps of around 10^-6 s and Brownian dynamics - can anyone comment on the advisability of these choices? I anticipate significant aggregation within ~seconds. Another issue is whether or not to include coarse-grained water and explicit ions in the simulation box. Recent postings on this list have suggested that Lagrangian dynamics should not be done in a vacuum, so presumably the same is true for Brownian dynamics? Has anyone on the list used 'coarse-grained' water in their GROMACS simulations (references needed)? If I have extracted different tabulated potentials for each background counterion concentration, this information is presumably 'built in' to my extracted PMF interparticle potentials, and I shouldn't need to include explicit counterions in my coarse-grained simulation, correct? Thank you for reading all the way through this posting. As mentioned in the message title, I will use and write up any advice given to me as a draft example tutorial on the wiki, then more qualified people can correct the (probably numerous) mistakes. Many thanks in advance, Steve Kirk -- Dr. Steven R. Kirk [EMAIL PROTECTED], [EMAIL PROTECTED] Dept. of Technology, Mathematics Computer Science (P)+46 520 223215 University West (F)+46 520 223299 P.O. Box 957 Trollhattan 461 29 SWEDEN http://taconet.webhop.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Coarse-graining and tabulated non-bonded potentials - will write
From: Steven Kirk [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] Coarse-graining and tabulated non-bonded potentials - will write up on the wiki Date: Mon, 26 Nov 2007 13:57:37 +0100 Hello all, Firstly, many thanks to everyone who has contributed useful advice to me over a number of years using GROMACS. I have performed a large number of potential of mean force calculations for the forces acting between two approximately spherical amorphous silica particles (various sizes 5 nm diameter) in TIP4P water with PME electrostatics and varying concentrations of background ions. Now I want to 'coarse-grain' the simulation, treating each silica particle as a single point mass, and use the interaction potential between the particles obtained from the PMF results as a tabulated potential in mdrun, to allow longer time- and size-scales to be investigated (I want to examine colloidal aggregation behaviour of these particles). I have tabulated the PMF potential and its derivatives as a function of centre-of-mass separation of the particles as suggested in the manual (but I can only tabulate for COM-COM distances greater than the contact distance [ = 2r in the hard-sphere approximation] out to some cutoff). Will I have to add a short-distance 'hard-sphere' wall to my tabulated potentials? I don't really understand the issue here. You (would) also directly get the repulsive part of the PMF from a constraint simulation. I assume that you mean that you have not done simulations to obtain the PMF at shorter distances? If not, just do so. I have read the appropriate section of the manual on tabulated interactions, and am working on building an appropriate topology. IU am assuming that my coarse-grained particles consist of the silica particles plus a number of surface counterions in such a way that the particles will be electrically neutral, so presumably I can set all the entries in the tabulated potential file for the Coulomb terms to zero. If my understanding of the manual is correct, I can then introduce my PMF potential in one or other of the g() and h() columns, along with its appropriate derivatives. The plan is to randomly place a number of the coarse-grained particles in a simulation box and choose an appropriate time step and thermostat to run aggregation simulations. Some of the literature I have read suggests timesteps of around 10^-6 s and Brownian dynamics - can anyone comment on the advisability of these choices? I anticipate significant aggregation within ~seconds. Another issue is whether or not to include coarse-grained water and explicit ions in the simulation box. Recent postings on this list have suggested that Lagrangian dynamics should not be done in a vacuum, so presumably the same is true for Brownian dynamics? Has anyone on the list used 'coarse-grained' water in their GROMACS simulations (references needed)? If I have extracted different tabulated potentials for each background counterion concentration, this information is presumably 'built in' to my extracted PMF interparticle potentials, and I shouldn't need to include explicit counterions in my coarse-grained simulation, correct? Because of the way you did things, everything is included in the PMF, both water and counterions. If this is an accurate approach is a completely different matter. Now you have the 2-body coarse-grained term correct, but there could of course be multi-body non-additive effects. For such effects you might need coarse-grained water or counterions, but then things get much more complicated. Berk. Thank you for reading all the way through this posting. As mentioned in the message title, I will use and write up any advice given to me as a draft example tutorial on the wiki, then more qualified people can correct the (probably numerous) mistakes. Many thanks in advance, Steve Kirk -- Dr. Steven R. Kirk [EMAIL PROTECTED], [EMAIL PROTECTED] Dept. of Technology, Mathematics Computer Science (P)+46 520 223215 University West (F)+46 520 223299 P.O. Box 957 Trollhattan 461 29 SWEDEN http://taconet.webhop.org ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the
Re: [gmx-users] Confusion Regarding Vacuum
On Mon, 26 Nov 2007 18:06:46 +0530 (IST) [EMAIL PROTECTED] wrote: Dear All, I am a bit confused regarding Vacuum. I wanted to do EM in Vacuum. I think I can proceed either of the below... 1) I create a box (editconf) and place a molecule with out solvent. 2) Never create a box, then proceed other steps as usual like EM etc. you should make sure your mdp file specifies no pbc: pbc = none Can we call 2nd option also a vacuum and what is more appropriate? Regards Chandu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to deduce charges for gromos forcefield?
Probably the easiest way for you to get an answer to this is to look up the references which discuss the parameterization of the GROMOS force field. Consistency is the name of the game. See here: http://wiki.gromacs.org/index.php/Parameterization David On Nov 25, 2007 1:21 AM, Q733 [EMAIL PROTECTED] wrote: Dear gmx-users, I want to develop an itp file for an organic molecule which has 87 atoms. I deduced the charge using the common Resp procedure with RED-III tool.However , I am not quite sure if the Resp charge or Esp charge can be used in Gromos forcefield, if not, how does Gromos forcefied deduce its charge distribution? Any suggestion will be appreciated, thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Can 1-4 interactions be excluded seperately?
Hi all, There are two molecules in my system. One is parameterized with no torsion term in the energy expression (consistent with the OPLS force field), so 1-4 interactions should be excluded. The other one is treated as a normal protein molecule using OPLS force field. I want to include OPLS ff, but not to gen pairs with the previous molecule. Does it feasible in gmx? Thanks in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] WCA potential
hi all, i am using a WCA potential and PME to calculate the non-bonded interactions of monomers of polyelectrolyte chains and counterions in solution. i use a table.xvg file where i have inserted the WCA potential (given values to x,f(x),f''(x),g(x),g''(x),h(x),h''(x) as is explained in the manual). is that the only way to insert the WCA potential in gromacs or i can do that automatically from the input file? Be a better sports nut! Let your teams follow you with Yahoo Mobile. Try it now. http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] WCA potential
From: Argyrios Karatrantos [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: gmx-users@gromacs.org Subject: [gmx-users] WCA potential Date: Mon, 26 Nov 2007 07:51:57 -0800 (PST) hi all, i am using a WCA potential and PME to calculate the non-bonded interactions of monomers of polyelectrolyte chains and counterions in solution. i use a table.xvg file where i have inserted the WCA potential (given values to x,f(x),f''(x),g(x),g''(x),h(x),h''(x) as is explained in the manual). is that the only way to insert the WCA potential in gromacs or i can do that automatically from the input file? That is (currently) the only way of doing it. But since Gromacs is becoming popular for coarse-grained simulations, we should consider writing special WCA loops. Berk. _ FREE pop-up blocking with the new Windows Live Toolbar - get it now! http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problems compiling GROMACS on IBM Blue Gene/L
Dear Gromacs-Users,
I'm hoping you can help.
I've tried compiling both version 3.3.1 and 3.3.2 of GROMACS on an IBM
Blue Gene/L system but get the same error message with each version. The
error is similar to that obtained by Hiroshi Fujisaki in thread:
http://www.gromacs.org/pipermail/gmx-users/2006-September/023957.html
Unfortunately no solution to this problem was ever posted to the list.
To compile the GROMACS I've used the following settings/configure flags.
export MPICC=mpixlc
export CC=blrts_xlc
export CXX=blrts_xlC
export F77=blrts_xlf
export LDFLAGS=${LDFLAGS} -L/bgl/local/lib/fftw/lib
export CPPFLAGS=${CPPFLAGS} -I/bgl/local/lib/fftw/include
export FFLAGS=-O3 -qarch=440 -qtune=440 -qmaxmem=-1 -qhot
export CFLAGS=-O3 -qarch=440 -qtune=440 -qmaxmem=-1 -qhot
** Note: mpixlc is a wrapper script which bundles up all the library paths
** to ensure they are linked in the correct order.
./configure --prefix=${PREFIX} --without-xml --without-x --with-fft=fftw2 --disable-float
--enable-mpi --program-suffix=_mpi_d --build=ppc-linux-gnu --host=powerpc
$LOGFILE
make mdrun
The error message I get is:
$ make mdrun
(cd ./src/gmxlib make ; exit 0)
make[1]: Entering directory `/home/b00/fiona/gromacs-3.3.1/src/gmxlib'
Making all in nonbonded
make[2]: Entering directory
`/home/b00/fiona/gromacs-3.3.1/src/gmxlib/nonbonded'
Making all in nb_kernel
make[3]: Entering directory
`/home/b00/fiona/gromacs-3.3.1/src/gmxlib/nonbonded/nb_kernel'
rm -f kernel-stamp
./mknb -double -software_invsqrt
Gromacs nonbonded kernel generator (-h for help)
Generating double precision functions in C.
Using Gromacs software version of 1/sqrt(x).
Error: Cannot open nb_kernel010_c.c for writing.
make[3]: *** [kernel-stamp] Error 1
make[3]: Leaving directory
`/home/b00/fiona/gromacs-3.3.1/src/gmxlib/nonbonded/nb_kernel'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory
`/home/b00/fiona/gromacs-3.3.1/src/gmxlib/nonbonded'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/b00/fiona/gromacs-3.3.1/src/gmxlib'
(cd ./src/mdlib make ; exit 0)
make[1]: Entering directory `/home/b00/fiona/gromacs-3.3.1/src/mdlib'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/home/b00/fiona/gromacs-3.3.1/src/mdlib'
(cd ./src/kernel make mdrun ; exit 0)
make[1]: Entering directory `/home/b00/fiona/gromacs-3.3.1/src/kernel'
make[1]: *** No rule to make target `../gmxlib/libgmx_mpi_d.la', needed by
`mdrun'. Stop.
make[1]: Leaving directory `/home/b00/fiona/gromacs-3.3.1/src/kernel'
Any help or suggestions would be much appreciated.
Thanks in advance,
Fiona
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Re: [gmx-users] Range checking error
Yanzi Zhou wrote: Dear Gromacs-Users, Can anybody help me? When I do 1 ns NTP MD simulation using version 3.3.2 on 4 or 6 processes with double precision gromacs compiled by Intel compiler on x86_64 GNU/Linux, it was crashing at about 100 ps with a message: --- Program mdrun_mpi_d, VERSION 3.3.2 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value 4421. It should have been within [ 0 .. 4212 ] --- But it can be finished when I use 1 or 2 processes, or use cut-off for electrostatics instead of PME, or for a NVT system, or with single precision gromacs. I have noticed the bug #167 on Bugzilla, and modified routine stat.c, but it did no help, and actually I didn't write to XTC file. Maybe, there are still bugs for double precision gromacs? More likely the compiler. Please retry with gcc. Thanks for any help. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error
Thank you. I recompiled the software with gcc, but my job still crashed at about 170ps. I tried 1 ns simulation for 1PGB in water downloaded from http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm, it can be finished. But when I tried to do NTP simulation of DPPC from the benchmarks of Gromacs, my job died on 6 processes with double precision gromacs. I found the job crashed when I: do NTP simulation for a large system, and use PME on more than two processors with double precision gromacs. David van der Spoel wrote: Yanzi Zhou wrote: Dear Gromacs-Users, Can anybody help me? When I do 1 ns NTP MD simulation using version 3.3.2 on 4 or 6 processes with double precision gromacs compiled by Intel compiler on x86_64 GNU/Linux, it was crashing at about 100 ps with a message: --- Program mdrun_mpi_d, VERSION 3.3.2 Source code file: nsgrid.c, line: 226 Range checking error: Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value 4421. It should have been within [ 0 .. 4212 ] --- But it can be finished when I use 1 or 2 processes, or use cut-off for electrostatics instead of PME, or for a NVT system, or with single precision gromacs. I have noticed the bug #167 on Bugzilla, and modified routine stat.c, but it did no help, and actually I didn't write to XTC file. Maybe, there are still bugs for double precision gromacs? More likely the compiler. Please retry with gcc. Thanks for any help. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Confusion Regarding Vacuum
[EMAIL PROTECTED] wrote: Dear All, I am a bit confused regarding Vacuum. I wanted to do EM in Vacuum. I think I can proceed either of the below... 1) I create a box (editconf) and place a molecule with out solvent. 2) Never create a box, then proceed other steps as usual like EM etc. Can we call 2nd option also a vacuum and what is more appropriate? A simulation in vacuo requires that you don't put a solvent in. A simulation with PBC requires that you choose the appropriate pbc option in your .mdp file, and also choose a sensible box size, e.g. with editconf. These two are independent choices. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] CNT Grompp errors and Force Field modifications
Ok I am trying to use the GROMOS96 43a1 force field to run a simulation of a finite CNT. I believe I have figured out how this force field can be modified. I have made the following additions to the respective 43a1 force field files and placed them in the root directory of the simulation: # *** ffG43a1bon.itp *** #define gb_48 0.142100 4.7890e+06 ; C - C #define ga_47 120.00 397.48 ; C - C - C *** ffG43a1.rtp *** [ UNK ] [ atoms ] [ bonds ] C C gb_48 [ angles ] C C C ga_47 [ impropers ] C C C 0 ga_1 *** ffG43a1.n2t *** C C 1 C ; CNT Carbon with one bond C C 2 C C : CNT double bonded Carbon # Note I also made the following change to ffG43a1bon.itp (the original line was): #define gd_1180.000 5.86 2 ; -C-C- 1.4 Now it is: #define gd_1167.360 5.86 2 ; -C-C- 1.4 I still get the following errors when I run grompp(here is the first 10): * WARNING 1 [file SWNT_6_6_144.top, line 167]: No default Bond types, using zeroes WARNING 2 [file SWNT_6_6_144.top, line 167]: No default Bond types for perturbed atoms, using normal values WARNING 3 [file SWNT_6_6_144.top, line 168]: No default Bond types, using zeroes WARNING 4 [file SWNT_6_6_144.top, line 168]: No default Bond types for perturbed atoms, using normal values WARNING 5 [file SWNT_6_6_144.top, line 169]: No default Bond types, using zeroes WARNING 6 [file SWNT_6_6_144.top, line 169]: No default Bond types for perturbed atoms, using normal values WARNING 7 [file SWNT_6_6_144.top, line 170]: No default Bond types, using zeroes WARNING 8 [file SWNT_6_6_144.top, line 170]: No default Bond types for perturbed atoms, using normal values WARNING 9 [file SWNT_6_6_144.top, line 171]: No default Bond types, using zeroes WARNING 10 [file SWNT_6_6_144.top, line 171]: No default Bond types for perturbed atoms, using normal values * At http://cs86.com/CNSE/CNT_FFOpt0.zip a zip file with all the files I use can be obtained, and the grompp command I use is: grompp -f md_200k.mdp -c SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top -maxwarn 10 -pp Also note I am working off the modifications I made to the Gromacs FF and they are as follows: * ffgmx.n2t and add the following 2 lines: C C 1 C ; CNT Carbon with one bond C C 2 C C ; CNT double bonded Carbon ffgmxbon.itp add the following line to it: *** To be very clear about this the first two lines are just telling what section to add it to in the file and what the units of that addition reprsent.*** # [ bondtypes ] ; i j func b0 kb C C 1 0.14210 478900. # [ angletypes ] ; i j k func th0 cth C C C 1 120.000 397.480 # [ dihedraltypes ] ; i l func q0 cq C C 1 0.000 167.360 # * Thank you very much for your help! ~Christopher Stiles College of Nanoscale Science and Engineering (CNSE) State University of New York, Albany, New York 12203, USA ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error
Yanzi Zhou wrote: Thank you. I recompiled the software with gcc, but my job still crashed at about 170ps. I tried 1 ns simulation for 1PGB in water downloaded from http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm, it can be finished. But when I tried to do NTP simulation of DPPC from the benchmarks of Gromacs, my job died on 6 processes with double precision gromacs. I found the job crashed when I: do NTP simulation for a large system, and use PME on more than two processors with double precision gromacs. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. What have you done to check that your system preparation protocol is reasonable? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Range checking error
I did MD simulation for lipid. I downloaded the pre-equilibrated structure and parameters from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies. I can do 5 ns NTP simulation with single precision, but it can't go on with double precision. I also tried the DPPC from the benchmarks of Gromacs. I first did the NTV simulation for 500 ps, and then do NTP simulation using PME, but crashed. Mark Abraham wrote: Yanzi Zhou wrote: Thank you. I recompiled the software with gcc, but my job still crashed at about 170ps. I tried 1 ns simulation for 1PGB in water downloaded from http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm, it can be finished. But when I tried to do NTP simulation of DPPC from the benchmarks of Gromacs, my job died on 6 processes with double precision gromacs. I found the job crashed when I: do NTP simulation for a large system, and use PME on more than two processors with double precision gromacs. Make sure your system is properly energy-minimized and that the potential energy seems reasonable before trying again. What have you done to check that your system preparation protocol is reasonable? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to solve this broken trjactory
Hello all, I am wondering if you can help me out with this trouble. I had a full disk space but my calculations finished as I can see from the log file. Several calculation continued to run and I freed some space and the calculation are still running. I tried to analysis the trjactory to see how the calculation is doing..but trjconv and gmxcheck gives me this error: Program trjconv, VERSION 3.3.1 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file Please help me out as I need to analyze these trjactories as they have been running for 4 weeks. thank you Belquis Mothana ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] pdb2gmx error
Hi,
I have just started to learn gromacs. I am facing a problem to make topology
file of a myoglobin. I got the pdb file from the csc tutorial.
When i am running the pdb2gmx with
pdb2gmx -f conf.pdb -p topol.top
i get the message, HEME148 CAB1428 0.569
HEME148 CAC1437 0.562 0.820
N-terminus: NH3+
C-terminus: COO-
Now there are 148 residues with 1451 atoms
---
Program pdb2gmx, VERSION 3.3.1
Source code file: pdb2top.c, line: 570
Fatal error:
atom N not found in residue 1ACE while combining tdb and rtp
---
I was using 43a1 force field (0), {but none of them works}.
i read some previous post and got the idea that there should be a N atom with
should be linked with ACE, but my conf.pdb files does not have any. I have
topol.top file from the tutorial but didn't show how I can generate that.
I am a totally newbie, thus I am wondering what should I do. Which file I
should correct to get rid of those? Do I need to know the bonding of every atom
in the molecule for that?
Thanks in advance
Tawhid
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Re: [gmx-users] pdb2gmx error
Quoting Tawhid Ezaz [EMAIL PROTECTED]:
Hi,
I have just started to learn gromacs. I am facing a problem to make topology
file of a myoglobin. I got the pdb file from the csc tutorial.
When i am running the pdb2gmx with
pdb2gmx -f conf.pdb -p topol.top
i get the message, HEME148 CAB1428 0.569
HEME148 CAC1437 0.562 0.820
N-terminus: NH3+
C-terminus: COO-
Now there are 148 residues with 1451 atoms
---
Program pdb2gmx, VERSION 3.3.1
Source code file: pdb2top.c, line: 570
Fatal error:
atom N not found in residue 1ACE while combining tdb and rtp
---
I was using 43a1 force field (0), {but none of them works}.
i read some previous post and got the idea that there should be a N atom with
should be linked with ACE, but my conf.pdb files does not have any. I have
topol.top file from the tutorial but didn't show how I can generate that.
Use the -ter option with pdb2gmx, and select 'none' when prompted. That way,
pdb2gmx does not look for an N-terminal nitrogen (which is obviously absent in
an acetyl group).
-Justin
I am a totally newbie, thus I am wondering what should I do. Which file I
should correct to get rid of those? Do I need to know the bonding of every
atom in the molecule for that?
Thanks in advance
Tawhid
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
___
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[gmx-users] Re:Moleculetype SOL contains no atoms
The top file is #include ffgmx.itp #include tip5P.itp [ system ] Pure water [ molecules ] SOL 258 - The itp file is [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; idat type res nr residu name at namecg nr charge #ifdef _FF_OPLS 1 opls_1181SOL OW 1 0 2 opls_1191SOL HW11 0.24 3 opls_1191SOL HW21 0.241 4 opls_1201SOL LP11 -0.241 5 opls_1201SOL LP21 -0.241 [ settles ] ; i funct doh dhh 1 1 0.09572 0.15139 [ dummies3 ] ; The position of the dummy is computed as follows: ; ; The distance from OW to OL is 0.07 nm, the geometry is tetrahedral ; (109.47 deg) ; Therefore, a =3D b =3D 0.07 * cos (109.47/2) / | xOH1 + xOH2 | ;c =3D 0.07 * sin (109.47/2) / | xOH1 X xOH2 | ; =20 ; ; Using | xOH1 X xOH2 | =3D | xOH1 | | xOH2 | sin (H1-O-H2) ; | xOH1 + xOH2 | =3D 2 | xOH1 | cos (H1-O-H2) ; Dummy pos x4 =3D x1 + a*x21 + b*x31 + c*(x21 X x31) ; Dummy fromfunct a b c 4 1 2 3 4 -0.344908 -0.344908 -6.4437903493 5 1 2 3 4 -0.344908 -0.344908 6.4437903493 [ exclusions ] 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 #endif Can anyone help me in this regard? Jestin Mandumpal___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx error
Thanks a lot Justin. It worked really nice.
now I am stuck with another problem. I need to add the Building block GTP and
GDP in 43a1, as I need to get the topology of a tubulin monomer. I got the
file from a old post here.
http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html
I copied and pasted it into my file, yet, as the structure doesn't match it
gave several errors.
is there any way to fix this?
Thanks a lot for your help.
Tawhid
- Original Message
From: Justin A. Lemkul [EMAIL PROTECTED]
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Monday, November 26, 2007 7:14:43 PM
Subject: Re: [gmx-users] pdb2gmx error
Quoting Tawhid Ezaz [EMAIL PROTECTED]:
Hi,
I have just started to learn gromacs. I am facing a problem to make
topology
file of a myoglobin. I got the pdb file from the csc tutorial.
When i am running the pdb2gmx with
pdb2gmx -f conf.pdb -p topol.top
i get the message, HEME148 CAB1428 0.569
HEME148 CAC1437 0.562 0.820
N-terminus: NH3+
C-terminus: COO-
Now there are 148 residues with 1451 atoms
---
Program pdb2gmx, VERSION 3.3.1
Source code file: pdb2top.c, line: 570
Fatal error:
atom N not found in residue 1ACE while combining tdb and rtp
---
I was using 43a1 force field (0), {but none of them works}.
i read some previous post and got the idea that there should be a N
atom with
should be linked with ACE, but my conf.pdb files does not have any. I
have
topol.top file from the tutorial but didn't show how I can generate
that.
Use the -ter option with pdb2gmx, and select 'none' when prompted.
That way,
pdb2gmx does not look for an N-terminal nitrogen (which is obviously
absent in
an acetyl group).
-Justin
I am a totally newbie, thus I am wondering what should I do. Which
file I
should correct to get rid of those? Do I need to know the bonding of
every
atom in the molecule for that?
Thanks in advance
Tawhid
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the
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Re: [gmx-users] how to solve this broken trjactory
Belquis Mothana wrote: Hello all, I am wondering if you can help me out with this trouble. I had a full disk space but my calculations finished as I can see from the log file. Several calculation continued to run and I freed some space and the calculation are still running. I tried to analysis the trjactory to see how the calculation is doing..but trjconv and gmxcheck gives me this error: Program trjconv, VERSION 3.3.1 Source code file: trnio.c, line: 66 File input/output error: Can not determine precision of trn file Please help me out as I need to analyze these trjactories as they have been running for 4 weeks. Well there's various lessons here. Whatever's been written to disk are the only resources you have. You can use gmxcheck to find out exactly what you have. Does the file have non-zero size? There may be some helpful information here http://wiki.gromacs.org/index.php/Doing_Restarts Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx error
Quoting Tawhid Ezaz [EMAIL PROTECTED]:
Thanks a lot Justin. It worked really nice.
now I am stuck with another problem. I need to add the Building block GTP and
GDP in 43a1, as I need to get the topology of a tubulin monomer. I got the
file from a old post here.
http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html
I copied and pasted it into my file, yet, as the structure doesn't match it
gave several errors.
is there any way to fix this?
That depends entirely upon what your errors are and what you're trying to do.
Please provide more details.
-Justin
Thanks a lot for your help.
Tawhid
- Original Message
From: Justin A. Lemkul [EMAIL PROTECTED]
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Monday, November 26, 2007 7:14:43 PM
Subject: Re: [gmx-users] pdb2gmx error
Quoting Tawhid Ezaz [EMAIL PROTECTED]:
Hi,
I have just started to learn gromacs. I am facing a problem to make
topology
file of a myoglobin. I got the pdb file from the csc tutorial.
When i am running the pdb2gmx with
pdb2gmx -f conf.pdb -p topol.top
i get the message, HEME148 CAB1428 0.569
HEME148 CAC1437 0.562 0.820
N-terminus: NH3+
C-terminus: COO-
Now there are 148 residues with 1451 atoms
---
Program pdb2gmx, VERSION 3.3.1
Source code file: pdb2top.c, line: 570
Fatal error:
atom N not found in residue 1ACE while combining tdb and rtp
---
I was using 43a1 force field (0), {but none of them works}.
i read some previous post and got the idea that there should be a N
atom with
should be linked with ACE, but my conf.pdb files does not have any. I
have
topol.top file from the tutorial but didn't show how I can generate
that.
Use the -ter option with pdb2gmx, and select 'none' when prompted.
That way,
pdb2gmx does not look for an N-terminal nitrogen (which is obviously
absent in
an acetyl group).
-Justin
I am a totally newbie, thus I am wondering what should I do. Which
file I
should correct to get rid of those? Do I need to know the bonding of
every
atom in the molecule for that?
Thanks in advance
Tawhid
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
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Re: [gmx-users] [Fwd: Semiisotropic pressure coupling comm_grps (VCM)]
Dear Xavier, Thanks a lot for your reply. I will follow your suggestions. Best Regards, Alok - Original Message - From: Xavier Periole [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, November 26, 2007 5:23 PM Subject: Re: [gmx-users] [Fwd: Semiisotropic pressure coupling comm_grps (VCM)] I have two basic questions regarding membrane protein simulation. First regarding Semiisotropic pressure coupling (NPAT) and second regarding comm_grpp (VCM). 1) If I want to use NPAT ensemble (x/y dimensions of bilayer to be fixed) then is following the correct way to define? Pcoupl = Berendsen Pcoupltype= semiisotropic tau_p = 2.0 2.0 compressibility = 04.5e-5 ref_p = 1.0 1.0 In some of the previous mails on same topic ref_p was defined as 0.0 1.0 in place of 1.0 1.0 even they was using compressibility 0.0 4.5e-5, that's why I am confuse. Do I have to take ref_p = 1.0 1.0 or 0.0 1.0 when I am using compressibility 0.0 4.5e-5 (NPAT). I think if I am taking compressibility value 0 then it doesn't matter what value I have taken for ref_p, but I want to confirm it. I would guess that ref_p = 1.0 1.0 and ref_p = 0.0 1.0 would give the result since you define compressibility = 0.0 4.5e-05 you can check that by running small trajectories ... 2) I want to remove center of mass translation so in following which one is better? a)comm_mode= Linear nstcomm = 1 comm_grps = Protein_POP ; (both protein and lipid are together) b)comm_mode= Linear nstcomm = 1 comm_grps = Protein POP ; (protein and lipid separately) It is better to remove the COM of both bilayer (plus protein) and the aqueous phase: comm_grps = Protein_POP SOL XAvier Thanks a lot Best Regards, Alok -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD NMR Molecular Dynamics Group University of Groningen The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] creating .tpr file
Dear Gromacs users, Using the command, grompp -f em.mdp -p topol.top -c out.gro -o pr.tpr, I wanted to build up tpr file for the simulation, but failed to do so. I received the error message : Moleculetype SOL contains no atoms. I paste my top files and .itp file below 1. TOP FILE ** #include ffgmx.itp #include tip5P.itp [ system ] Pure water [ molecules ] SOL 258 - The itp file is [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; idat type res nr residu name at namecg nr charge #ifdef _FF_OPLS 1 opls_1181SOL OW 1 0 2 opls_1191SOL HW11 0.24 3 opls_1191SOL HW21 0.241 4 opls_1201SOL LP11 -0.241 5 opls_1201SOL LP21 -0.241 [ settles ] ; i funct doh dhh 1 1 0.09572 0.15139 [ dummies3 ] ; The position of the dummy is computed as follows: ; ; The distance from OW to OL is 0.07 nm, the geometry is tetrahedral ; (109.47 deg) ; Therefore, a =3D b =3D 0.07 * cos (109.47/2) / | xOH1 + xOH2 | ;c =3D 0.07 * sin (109.47/2) / | xOH1 X xOH2 | ; =20 ; ; Using | xOH1 X xOH2 | =3D | xOH1 | | xOH2 | sin (H1-O-H2) ; | xOH1 + xOH2 | =3D 2 | xOH1 | cos (H1-O-H2) ; Dummy pos x4 =3D x1 + a*x21 + b*x31 + c*(x21 X x31) ; Dummy fromfunct a b c 4 1 2 3 4 -0.344908 -0.344908 -6.4437903493 5 1 2 3 4 -0.344908 -0.344908 6.4437903493 [ exclusions ] 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 #endif Can anyone help me in this regard? Jestin Mandumpal ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
