[gmx-users] Fatal error in popc simulation: Atomtype LC3 not found
Dear gmx users, I want to simulate popc in water. What I have done is: 1.Build the popc.top file using the popc.itp parameters and including gmx.ff, lipid.itp and spce.itp in it as below; ; Include forcefield parameters #include ./gmx.ff/forcefield.itp ; Include water topology #include ./gmx.ff/spce.itp #include lipid.itp [ moleculetype ] ; Name nrexcl POPC 3 [ atoms ] ; nr type resnr residu atom cgnr charge mass 1 LC3 1 POP C1 0 0.4000 15.0350 ; qtot:0.36 2 LC3 1 POP C2 0 0.4000 15.0350 ; qtot:0.72 . . . [ bonds ] ; ai aj funct 4 5 1 0.14700E+00 0.37660E+06 5 6 1 0.15300E+00 0.33470E+06 6 7 1 0.14300E+00 0.25100E+06 . . . [ pairs ] ; ai aj funct 1 6 1 2 6 1 . . . [ angles ] ; ai aj ak funct 4 5 6 1 0.10950E+03 0.46020E+03 5 6 7 1 0.10950E+03 0.46020E+03 6 7 8 1 0.12000E+03 0.39750E+03 7 8 9 1 0.10960E+03 0.39750E+03 48 49 50 1 0.11100E+03 0.46020E+03 1 4 2 1 0.10950E+03 0.33470E+03 2 4 3 1 0.10950E+03 0.33470E+03 3 4 1 1 0.10950E+03 0.33470E+03 1 4 5 1 0.10950E+03 0.37660E+03 2 4 5 1 0.10950E+03 0.37660E+03 3 4 5 1 0.10950E+03 0.37660E+03 [ dihedrals ] ; ai aj ak al funct phi0 cp mult 1 4 5 6 1 0.0 3.76 3 4 5 6 7 1 0.0 5.85 3 . . . [ dihedrals ] ; ai aj ak al funct 13 14 32 12 2 35.264 0.33470E+03 15 14 17 16 2 0.0E+00 0.16740E+03 34 33 36 35 2 0.0E+00 0.16740E+03 23 24 25 26 2 0.000 167.360 [ system ] ; name POPC in water [ molecules ] ; name number POPC 128 SOL 3802 But I still get the fatal error : Atomtype LC3 not found . What is the problem? Anybody may help me please? Thanks in advance, Shima-- 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] Gromacs 4.6 with CUDA 4.2
Dear all, will the new version 4.6 work together with CUDA 4.2? Would be good to know, since this is needed for the new NVIDIA Gemini cards with Kepler technology. Thanks, Basti -- 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] extra factor in PMF
The factor depends on the choice of your reaction coordinate, and since g_wham doesn't care about it - it's not included. It accounts for the change in volume when going from cartesian to general coordinates and can be computed as -k_B * T * (d ln ( | J |) / d_lambda), where lambda is the function of atomic coordinates and | J | the determinant of the Jacobian matrix. (C. Chipot and A. Pohorille, editors. Free Energy Calculations: Theory and Applications in Chemistry and Biology. Springer Series in Chemical Physics (Springer), 2007.) Best wishes Martin -- 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] Fatal error in popc simulation: Atomtype LC3 not found
On 4/25/12 2:07 AM, Shima Arasteh wrote: Dear gmx users, I want to simulate popc in water. What I have done is: 1.Build the popc.top file using the popc.itp parameters and including gmx.ff, lipid.itp and spce.itp in it as below; ; Include forcefield parameters #include ./gmx.ff/forcefield.itp ; Include water topology #include ./gmx.ff/spce.itp #include lipid.itp [ moleculetype ] ; Name nrexcl POPC 3 [ atoms ] ; nr type resnr residu atom cgnr charge mass 1 LC3 1 POP C1 0 0.4000 15.0350 ; qtot:0.36 2 LC3 1 POP C2 0 0.4000 15.0350 ; qtot:0.72 . . . [ bonds ] ; ai aj funct 4 5 1 0.14700E+00 0.37660E+06 5 6 1 0.15300E+00 0.33470E+06 6 7 1 0.14300E+00 0.25100E+06 . . . [ pairs ] ; ai aj funct 1 6 1 2 6 1 . . . [ angles ] ; ai aj ak funct 4 5 6 1 0.10950E+03 0.46020E+03 5 6 7 1 0.10950E+03 0.46020E+03 6 7 8 1 0.12000E+03 0.39750E+03 7 8 9 1 0.10960E+03 0.39750E+03 48 49 50 1 0.11100E+03 0.46020E+03 1 4 2 1 0.10950E+03 0.33470E+03 2 4 3 1 0.10950E+03 0.33470E+03 3 4 1 1 0.10950E+03 0.33470E+03 1 4 5 1 0.10950E+03 0.37660E+03 2 4 5 1 0.10950E+03 0.37660E+03 3 4 5 1 0.10950E+03 0.37660E+03 [ dihedrals ] ; ai aj ak al funct phi0 cp mult 1 4 5 6 1 0.0 3.76 3 4 5 6 7 1 0.0 5.85 3 . . . [ dihedrals ] ; ai aj ak al funct 13 14 32 12 2 35.264 0.33470E+03 15 14 17 16 2 0.0E+00 0.16740E+03 34 33 36 35 2 0.0E+00 0.16740E+03 23 24 25 26 2 0.000 167.360 [ system ] ; name POPC in water [ molecules ] ; name number POPC 128 SOL 3802 But I still get the fatal error : Atomtype LC3 not found . What is the problem? Anybody may help me please? I always had problems when trying to simply #include lipid.itp - the directives are not in the proper order for the system .top if you do. The better approach is to append the contents of lipid.itp to the appropriate directives in ffnonbonded.itp and ffbonded.itp. See the approach in: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] paluso...@gmail.com
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[gmx-users] Fatal error
Respected sir, While i am running the gromacs always i am getting the error Residue 'GNP' not found in residue topology database.Kindly tell me the what the error means. Suryanarayana Seera, -- 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] Fatal error
On 4/25/12 8:19 AM, seera suryanarayana wrote: Respected sir, While i am running the gromacs always i am getting the error Residue 'GNP' not found in residue topology database.Kindly tell me the what the error means. http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Gromacs 4.6 with CUDA 4.2
On Wed, Apr 25, 2012 at 11:43 AM, SebastianWaltz sebastian.wa...@physik.uni-freiburg.de wrote: Dear all, will the new version 4.6 work together with CUDA 4.2? Would be good to know, since this is needed for the new NVIDIA Gemini cards with Kepler technology. Yes it will. I would like to point out that the needed part is not exactly true, binaries compiled with pre-4.2 can run equally fast on Kepler especially if JIT compilation of PTX code is enabled. Moreover, current 4.2 pre-release compiler produces slower code than CUDA 4.0 not only for Fermi but also for Kepler. We'll have to see brins the final CUDA 4.2 release + official drivers. -- Szilárd Thanks, Basti -- gmx-users mailing list gmx-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] a question about energygrps
Hello: I am running a membrane simulation with gromacs and I wondering how to deal with energygrps? Should I put protein and lipids into one energygrps? Or I should leave the lipids stay with solvent and ions? thank you very much best Albert -- 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] a question about energygrps
On 4/25/12 10:07 AM, Albert wrote: Hello: I am running a membrane simulation with gromacs and I wondering how to deal with energygrps? Should I put protein and lipids into one energygrps? Or I should leave the lipids stay with solvent and ions? You can divide the system in any way you like for energygrps; it's just a decomposition of the nonbonded terms. The way your break it down depends on what you care to measure in the system. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] a question about energygrps
hello Justin: thank you very much for kind reply. In gromacs tutorial I found that the author use the following paramters: tc-grps= Protein DPPC SOL_CL; three coupling groups - more accurate comm-grps= Protein_DPPC SOL_CL do you have any idea why did he use different groups for above paramters in NVT.mdp? thank you very much On 04/25/2012 04:13 PM, Justin A. Lemkul wrote: On 4/25/12 10:07 AM, Albert wrote: Hello: I am running a membrane simulation with gromacs and I wondering how to deal with energygrps? Should I put protein and lipids into one energygrps? Or I should leave the lipids stay with solvent and ions? You can divide the system in any way you like for energygrps; it's just a decomposition of the nonbonded terms. The way your break it down depends on what you care to measure in the system. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] a question about energygrps
On 4/25/12 10:20 AM, Albert wrote: hello Justin: thank you very much for kind reply. In gromacs tutorial I found that the author use the following paramters: tc-grps = Protein DPPC SOL_CL ; three coupling groups - more accurate comm-grps = Protein_DPPC SOL_CL OK, just so we're clear: tc-grps, comm-grps, and energygrps are all wildly different concepts, so don't get them confused. do you have any idea why did he use different groups for above paramters in NVT.mdp? Indeed I do - I wrote it ;) Ideally, one would like to use a single thermostat for the whole system, but in practice, especially for heterogeneous systems, the heat exchange between different groups can be different. Hence the protein, lipids, and aqueous solvent are coupled separately. They are of sufficient size to justify their own group (note, for instance, that ions are not coupled separately). With respect to the comm-grps, since the system is basically an interface, the lipids and aqueous layers can slide with respect to one another, generating no net COM motion, but each layer may actually be have a net velocity, which would lead to artifacts. -Justin thank you very much On 04/25/2012 04:13 PM, Justin A. Lemkul wrote: On 4/25/12 10:07 AM, Albert wrote: Hello: I am running a membrane simulation with gromacs and I wondering how to deal with energygrps? Should I put protein and lipids into one energygrps? Or I should leave the lipids stay with solvent and ions? You can divide the system in any way you like for energygrps; it's just a decomposition of the nonbonded terms. The way your break it down depends on what you care to measure in the system. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] a question about energygrps
hello Justin: thank you very much for your such kind explanations. It is quite helpful. I am wondering how many CPU did you usually use for the membrane simulations? and how many ns/day can you get the best if CPU is not a problem with Gromacs? I am very confused about this question since some one claimed that they can use optimized PMF/F paramters to achieve even 100ns/day for 20,000 atoms system. I also try to use g_tune_pme to get a better performance, but the results are not so satisfied.. Can you give me some advices for this? thank you very much. best Albert On 04/25/2012 04:34 PM, Justin A. Lemkul wrote: Indeed I do - I wrote it ;) Ideally, one would like to use a single thermostat for the whole system, but in practice, especially for heterogeneous systems, the heat exchange between different groups can be different. Hence the protein, lipids, and aqueous solvent are coupled separately. They are of sufficient size to justify their own group (note, for instance, that ions are not coupled separately). With respect to the comm-grps, since the system is basically an interface, the lipids and aqueous layers can slide with respect to one another, generating no net COM motion, but each layer may actually be have a net velocity, which would lead to artifacts. -Justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] RE: Potential bug? Different results from different versions of gromacs with cos_acceleration
Just a follow up on this problem. I think it is known that there is some bug in the 1/viscosity calculation in Gromacs version of 4.5.3. As shown in the following posts in the mailing list:1. lists.gromacs.org/pepermail/gmx-users/2011-January/057596.html2. lists.gromacs.org/pepermail/gmx-users/2011-March/059475.html But both of them report the g_energy gives 1/viscosity as zero in the outcome, which is different from the case I reported here. Now with Gromacs 4.5.5, the previous bug could have been fixed. As stated in the release notes for 4.5.4, it says Fixed incorrect cosine viscosity output. However, the output now is not zero but a number (viscosity) far too high compared to results from a different calculation method and an older version (3.3.3). Could it be a new bug in Gromacs 4.5.5? One more details in the calculation with the periodic perturbation method: Since I am running NEMD and the method with Green-Kubo relation is for equilibrium MD, I just use g_energy without -vis. Thanks,Zhe From: zephyr...@hotmail.com To: gmx-users@gromacs.org Subject: Potential bug? Different results from different versions of gromacs with cos_acceleration Date: Wed, 25 Apr 2012 10:45:30 +0800 Dear Gromacs users and developers, I found Gromacs 4.5.5 problematic in NEMD calculations for viscosity. As a simple benchmark, I did some calculations for water (TIP5P) and the results are confusing. I applied two methods for the calculation in 300K, 512 waters: 1. momentum fluctuations, 2. periodic pertubation method, with Gromacs 4.5.5 double precision, each for 500 ps. (I understand it's short but it is just for benchmark and a longer calculation won't change the result qualitatively.) The first one is an equilibrium simulation (saving coordinates and velocity every 10 fs) and gives results as eta = 0.564 X 10^(-3) kg/(m * s), from the fitting of eta(k)=eta*(1-A*k^2) from g_tcaf, which is reasonable compared to experimental results and TIP5P results from earlier work. However, with periodic pertubation method, which is NEMD with cos_acceleration = 0.025 nm*ps^(-2) according to the original paper for SPC water, the result from g_energy gives 1/Viscosity as 103.276 m*s/kg. That means the viscosity is 9.68 X 10^(-3) kg/(m * s), which is an order of magnitude higher compared to the previous result! (Such result is reproduced for larger system, different cos_acceleration ( 1 nm*ps^(-2)) and longer runs.) As a next step, I went into the code in mdlib and found that the code is relatively old. (I searched the mailing list and found most posts about such method is around 2007, and the ones around 2010 mentioning the similar observation but not responded.) So I used Gromacs 3.3.3 with the same inputs as previous for NEMD and performed the simulation again. Now with g_energy, 1/Viscosity is 2080.94 m*s/kg. (It doesn't mention specifically in the output for the unit, as stated as SI unit. So it should be m*s/kg, right?) Then the viscosity is 0.481 X 10^(-3) kg/(m * s), and qualitatively agrees with the previous results. The original paper: http://jcp.aip.org/resource/1/jcpsa6/v116/i1/p209_s1 So the question is: Am I doing anything wrong? Or is the unit for viscosity in 3.3.3 different from 4.5.5? Or is NEMD just not a good method to calculate viscosity? (For the last question, it seems to be an open field for research.) I have to admit that the fluctuation of the results is very large (may due to the short simulation with small box) but I don't think it will change the results qualitatively. Any suggestions will be really appreciated. Thank you in advanced for your help! Thanks,Zhe -- 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] a question about energygrps
On 4/25/12 10:49 AM, Albert wrote: hello Justin: thank you very much for your such kind explanations. It is quite helpful. I am wondering how many CPU did you usually use for the membrane simulations? and how many ns/day can you get the best if CPU is not a problem with Gromacs? I am very confused about this question since some one claimed that they can use optimized PMF/F paramters to achieve even 100ns/day for 20,000 atoms system. I also try to use g_tune_pme to get a better performance, but the results are not so satisfied.. Can you give me some advices for this? I have never been able to get anywhere close to such performance for explicit solvent calculations using PME. Maybe others who have can describe their experience. I don't have an exact benchmark for the tutorial runs, but 24 CPU's gave somewhere in the ballpark of 10-15 ns/day on our (relatively old) hardware. My rule of thumb is 1000 atoms/CPU, and then tweak from there if necessary. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Error in MD simulation
Hi all!! I am running a MD simulation of a protein modelled by using modeller...and I am getting an error in the grompp command. The error reported was : Number of coordinates in coordinate file (z_b4em.gro) does not match that of topology file (z.top). We are however not able to run the nohup command because of the above mentioned error. The link for em.mdp and the output obtained is : http://s1064.photobucket.com/albums/u378/vinee2here/ Your help in resolving this issue would be highly appreciated. Thanking you. Vineetha -- View this message in context: http://gromacs.5086.n6.nabble.com/Error-in-MD-simulation-tp4917259p4917259.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error in MD simulation
On 4/25/12 12:45 PM, vinee2here wrote: Hi all!! I am running a MD simulation of a protein modelled by using modeller...and I am getting an error in the grompp command. The error reported was : Number of coordinates in coordinate file (z_b4em.gro) does not match that of topology file (z.top). We are however not able to run the nohup command because of the above mentioned error. The link for em.mdp and the output obtained is : http://s1064.photobucket.com/albums/u378/vinee2here/ Your help in resolving this issue would be highly appreciated. The fatal error should have also printed a URL that you can follow to find this information: http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology The solution to that particular error is always the same - keep track of your molecules better. Use of the -p flag with genbox and genion to allow the programs to do the bookkeeping for you eliminates the majority of the problems. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] Free Energy calcualtions
Hi Gromacs Users, I want to mutate a glutamate in my protein to alanine in presence of a ligand. With glutamate, the protein charge is -3. To neutralize the system, I added 3K+ ions. Now when I mutate GLU to ALA, the charge in state_B will be +1 (protein -2 + 3K+). Right now I'm in the charge part of the mutation. Once this is successful, I will include the VDW mutation too. I have added the mutation details of Glu to Ala residue in the topology in [atoms], [bonds], [angles] and [dihedrals] sections. After I run the grompp command, the result says that my State_B topology has +1 charge since I am not including mutation of one K+ ion to neutral K+ ion. How can I mutate 1 particular K+ to K atom and subsequently to a dummy atom? Since I'm using OPLS force field, we have ions.itp to be used in the topology file, changing one K+ is making it troublesome for me to implement in the topology file. Any suggestions are helpful. Thanks for your time. Regards Sai -- 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 choose two atoms at the same time, using g_select selection.dat
Dear gmx users, I may have a silly question, how to make a group of two atoms from the same molecule? e.g, I want to make an HN group of both H and N from my 2nd residue, I know for single one, commands in *.dat file is like: nameN = resnr 2 and name N; nameH = resnr 2 and name H; nameN; nameH; I guess merge or plus might be helpful,I think it should be done something like: nameN_H = resnr 2 and name N ?? resnr 2 and name H, so it is an intramolecular combination between N and H; it shouldn't be done afterwards, otherwise it would be an intermolecular combination. Thanks very much! g_select is really powerful, and hopefully there would be more examples. Jia -- 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] How to choose two atoms at the same time, using g_select selection.dat
On 4/25/12 9:19 PM, mu xiaojia wrote: Dear gmx users, I may have a silly question, how to make a group of two atoms from the same molecule? e.g, I want to make an HN group of both H and N from my 2nd residue, I know for single one, commands in *.dat file is like: nameN = resnr 2 and name N; nameH = resnr 2 and name H; nameN; nameH; I guess merge or plus might be helpful,I think it should be done something like: nameN_H = resnr 2 and name N ?? resnr 2 and name H, so it is an intramolecular combination between N and H; it shouldn't be done afterwards, otherwise it would be an intermolecular combination. Thanks very much! g_select is really powerful, and hopefully there would be more examples. g_select is more suited for complex groups that are dynamic or otherwise based on geometric criteria. If you're trying to make a simple group that consists of 2 atoms, make_ndx is easier, and using a plain text editor will be easiest, i.e.: [ my_group ] 1 2 -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] why it is so slow in Blue gene?
On 25/04/2012 3:24 PM, Albert wrote: hello: it is blue gene P. And the gromacs is single precision in the cluster. Getting Loaded...And the administrator told me that I have to use the multiples of 32 in the bg_size parameter. The number specified in -np should be 4 times bg_size. Yes, but your system is too small to make use of 128 processors. Also, get rid of -launch and -nt from your command line, since they do nothing. It is even slower than my own workstation with 16 core. here is the log file I get: No, that's the stdout file. Look at the end of the .log file. -log Reading file npt_01.tpr, VERSION 4.5.5 (single precision) Loaded with Money Will use 112 particle-particle and 16 PME only nodes This is guaranteed to lead to woeful performance with your .mdp settings, but you will have to look towards the beginning of the .log file to find out why mdrun selected this. Odds are good that your system size is so small that the minimum particle-particle cell size (constrained by rcoulomb) doesn't give mdrun any good options that use all the processors. You'd likely get better raw performance with twice the number of atoms or half the number of processors. Mark This is a guess, check the performance at the end of the log file Making 3D domain decomposition 4 x 4 x 7 starting mdrun 'GRowing Old MAkes el Chrono Sweat' 50 steps,500.0 ps. step 0 vol 0.64! imb F 16% pme/F 0.22 step 100, will finish Wed Apr 25 18:28:06 2012 vol 0.65! imb F 17% pme/F 0.21 step 200, will finish Wed Apr 25 18:09:54 2012 vol 0.67! imb F 18% pme/F 0.21 step 300, will finish Wed Apr 25 18:03:12 2012 vol 0.69! imb F 18% pme/F 0.21 step 400, will finish Wed Apr 25 17:58:25 2012 vol 0.67! imb F 19% pme/F 0.21 step 500, will finish Wed Apr 25 17:55:26 2012 vol 0.68! imb F 19% pme/F 0.22 step 600, will finish Wed Apr 25 17:53:31 2012 vol 0.68! imb F 19% pme/F 0.22 step 700, will finish Wed Apr 25 17:51:57 2012 vol 0.68! imb F 19% pme/F 0.22 step 800, will finish Wed Apr 25 17:50:32 2012 vol 0.68! imb F 20% pme/F 0.22 step 900, will finish Wed Apr 25 17:49:14 2012 vol 0.67! imb F 21% pme/F 0.22 step 1000, will finish Wed Apr 25 17:48:13 2012 vol 0.68! imb F 20% pme/F 0.22 step 1100, will finish Wed Apr 25 17:47:28 2012 vol 0.67! imb F 21% pme/F 0.22 step 1200, will finish Wed Apr 25 17:46:50 2012 vol 0.67! imb F 21% pme/F 0.22 step 1300, will finish Wed Apr 25 17:46:15 2012 On 04/24/2012 06:01 PM, Hannes Loeffler wrote: On Tue, 24 Apr 2012 15:42:15 +0200 Albertmailmd2...@gmail.com wrote: hello: I am running a 60,000 atom system with 128 core in a blue gene cluster. and it is only 1ns/day here is the script I used for You don't give any information what exact system that is (L/P/Q?), if you run single or double precision and what force field you are using. But for a similar sized system using a united atom force field in single precision we find about 4 ns/day on a BlueGene/P (see our benchmarking reports on http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx). I would expect a run with the CHARMM 27 force field in double precision to be roughly 3 times slower. We found scaling to 128 cores to be reasonably good. Also, check our report for problems when compiling with higher optimisation. Hannes. -- 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] Fwd: Error: coordinate file does not match with the topology file
Please do not make unsolicited general GROMACS inquiries to private email addresses. The mailing lists exist for these kinds of purposes. On point, you cannot be helped unless you provide the command lines that you used and describe the objectives you were trying to achieve. Whatever changes you make to one of the coordinate and .top file must be matched in the other. Mark Original Message Subject:Error: coordinate file does not match with the topology file Date: Wed, 25 Apr 2012 02:05:45 +0800 (SGT) From: sonali shinde shindesonal...@yahoo.co.in Reply-To: sonali shinde shindesonal...@yahoo.co.in To: mark.abra...@anu.edu.au mark.abra...@anu.edu.au - Forwarded Message - *From:* sonali shinde shindesonal...@yahoo.co.in *To:* vini k vineetha_mand...@yahoo.co.in *Sent:* Monday, 23 April 2012 6:48 PM *Subject:* Error: coordinate file does not match with the topology file Dear Sir, I am a user of gromacs 4.0 for molecular dynamic study of a protein molecule. I have generated trajectory file before using the same commands that I use now. Recently I am suffering some problem using Gromacs , my coordinate file does not matches with the topology file.I have attached the pdb file protein, .gro and .top file . I have encountered same error a number of times with three different proteins.Please suggest the answer for the same. Thanking you. -- 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] How to increase the ratio of cell size to constrain length per error message
On 25/04/2012 6:28 AM, PAVAN PAYGHAN wrote: Dear Gromacs Users, I am using gromacs version is 4.5.3.and running my jobs on single node with 8 cores. I have two different systems which contain about 425000 atoms (protein + Lipid +SOL) one with bound ligand and another one unbound protein.I have successfully reached up to NPT equilibration run step, It is a poor idea to do equilibration with Parinello-Rahman, which is unstable when the system is not already close to equilibrium. For some reason people still do it, despite at least a post per week on this list suggesting against it, and a warning in the manual. Use Berendsen to fix the density, then equilibrate further with P-R to get the right ensemble. now I want to continue the same for production run. Without ligand I am able to run successfully But the same system with ligand is crashing with following error- D D cell 1 0 0 could only obtain 1520 of the 1521 atoms that are are connected via constraints from the neighbouring cells This probably means your constraint length are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or lincs_order. I'd rather expect your system was blowing up because of the above issue. Perhaps the suggestion in the error message is not as complete as could be desired - you have so many atoms per processor that the constraint length would normally be tiny with respect to the cell size. So I think the things you have tried below are rearranging the deck chairs on the Titanic. Mark Accordingly following the suggestions given in the error I tried to solve it with Following log file and changed, 1.1. -rcon Estimated maximum distance required for p-lincs was 0.877 thus I increased it to 0.900 then it thrown another error. The initial cell size (0.877) is smaller than the cell size limit (0.900) 2 .Then I tried to increase the --dds and --rdd from original values of 1.25 and 0.623 to 1.30 and 0.670 respectively. But it does not help and ended with run crash. /*What I did was logical or I did it wrongly?*/ /*Now can anyone please suggest me the appropriate way to deal with the problem mentioned above? */ As I want the continuation of the same run without altering the output after change in the parameters (As I have to compare the output with unbound protein run thus can't afford change in output with change in parameters) I know that I need to change some of the parameters in .mdp file such as fourierspacing from 0.16 to 0.12 and on the contrary increase the pme_order from say 4 to 6. /*But as asked above by doing so the output will not or will be the exact continuation run?*/ /*How to increase the ratio of cell size to constrain length per error message?*/ /*If any better way of doing so without changing the output please suggest,*/ I am suffering from the same problem since long, Please help me .Please see the mdp file for the reference. integrator= md nsteps = 1000 dt = 0.002 ; 2 fs ; Output control nstxout= 1000; nstvout = 1000; nstxtcout = 1000; nstenergy= 1000; nstlog = 1000; ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; Neighborsearching ns_type = grid nstlist = 5 rlist= 1.2 rcoulomb= 1.2 rvdw= 1.2 ; Electrostatics coulombtype = PME pme_order = 4 fourierspacing = 0.16 tcoupl = Nose-Hoover tc-grps= Protein PSOL_NA_CL ; tau_t= 0.5 0.5 0.5 ref_t= 323 323 323 group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; pcoupltype = semiisotropic tau_p = 2.0 ; time ref_p = 1.0 1.0 ; reference compressibility = 4.5e-5 4.5e-5 ; ; Periodic boundary conditions pbc = xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel = no Thanking in Advance -- 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.
