RE: [gmx-users] Monte Carlo with Gromacs and implicit solvent
Hi Gianluca, I have no experience with the -rerun option of mdrun, but my guess is that an integrated MC/NVT algorithm in GromPy will be faster. For CGMC, a trial configuration involves generating a new tpr file using grompp, either with N+1 or N-1 molecules of interest. I implemented such a shell approach to compare it to GromPy. It turns out that GromPy is 14 times faster compared to the shell approach for system sizes of about 500 molecules. This speed-up factor increases with increasing system size. This all is due to the fact that tpr's are kept in memory during run time in GromPy. The shell approach on the other hand uses up a lot of computer time for e.g. file I/O. The above is based on the GCMC case so it would not necessarily have to apply to MC/NVT. Cheers, Rene = René Pool Division of Molecular and Computational Toxicology Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit Amsterdam De Boelelaan 1083 1081HV AMSTERDAM, the Netherlands - IBIVU/Bioinformatics Department of Computer Science Vrije Universiteit Amsterdam De Boelelaan 1081a 1081HV AMSTERDAM, the Netherlands Room P 2.75 E: r.p...@vu.nl T: +31 20 598 76 12 F: +31 20 598 76 10 = From: Gianluca Interlandi [gianl...@u.washington.edu] Sent: 31 January 2012 19:55 To: Pool, R. Cc: Discussion list for GROMACS users Subject: RE: [gmx-users] Monte Carlo with Gromacs and implicit solvent Hi Rene, Thanks for your reply. One question though. How much overhead do you think I would have in calling mdrun -rerun after every step and would it run more efficiently if I used GromPy? Thanks, Gianluca On Tue, 31 Jan 2012, Pool, R. wrote: Hi Gianluca, Ah, I get it. In that case you can actually use GromPy, but it needs to be modified slightly. You need only one tpr file that will be stored in memory during execution of GromPy. For the sampling you can generate new configurations and accept/reject them according to the appropriate rules. The coordinates/velocities have to be put back in the tpr data structure before calculating the energy. You have to write a routine that generates a new configuration yourself, but that should not be too hard. Obviously, the Monte Carlo acceptance rules have to be adjusted for sampling in the NVT ensemble. The alternative is mdrun -rerun as suggested before. Cheers, René = René Pool Division of Molecular and Computational Toxicology Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit Amsterdam De Boelelaan 1083 1081HV AMSTERDAM, the Netherlands - IBIVU/Bioinformatics Department of Computer Science Vrije Universiteit Amsterdam De Boelelaan 1081a 1081HV AMSTERDAM, the Netherlands Room P 2.75 E: r.p...@vu.nl T: +31 20 598 76 12 F: +31 20 598 76 10 = From: Gianluca Interlandi [gianl...@u.washington.edu] Sent: 30 January 2012 17:36 To: Pool, R. Cc: Discussion list for GROMACS users Subject: RE: [gmx-users] Monte Carlo with Gromacs and implicit solvent Hi René, I want to perform simulations of a protein near a surface, for example silicates. The surface is fixed and the protein is treated as a rigid body. Solvation is treated with GBSA implicit model. The point is to sample orientations of the protein with respect to the surface using Monte Carlo moves. I guess I am sampling the canonical ensemble. Gianluca On Mon, 30 Jan 2012, Pool, R. wrote: Hi Gianluca, The tutorial involves simulations using a simple LJ model. GromPy/GCMC has been validated by comparing equations of state, calculated using MD in the NVT ensemble and GromPy in the muVT ensemble, for both the LJ and SPC fluids. For both models, the muVT and NVT results are in agreement. Therefore, in principle, you can use GromPy for more sophisticated molecular models. Which ensemble are you intending to use? Cheers, René = René Pool Division of Molecular and Computational Toxicology Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit Amsterdam De Boelelaan 1083 1081HV AMSTERDAM, the Netherlands - IBIVU/Bioinformatics Department of Computer Science Vrije Universiteit Amsterdam De Boelelaan 1081a 1081HV AMSTERDAM, the Netherlands Room P 2.75 E: r.p...@vu.nl T: +31 20 598 76 12 F: +31 20 598 76 10 = From: Gianluca Interlandi [gianl...@u.washington.edu] Sent: 24 January 2012 21:20 To: Pool, R.; Discussion list for GROMACS users Subject: Re: [gmx-users] Monte Carlo with Gromacs and implicit solvent Hi Renè, This might be a silly question. In the
[gmx-users] Pulling multiple groups
Hi I am trying to use the pull code of gromacs (version 4.5.5) to constrain the com of a number of groups (labelled CIT, CIT1, CIT2...) to a reference group (labelled GOLD). This is the segment of the .mdp file I have used: ;CoM pull calculations pull= constraint pull_geometry = distance pull_dim= N N Y pull_constr_tol = 1e-6 ; add COM distance of starting config to pull_init pull_start = yes ;frequency for writing COMS of all pull group pull_nstxout= 10 ;frequency for writing force of all pull group pull_nstfout= 10 pull_ngroups= 12 ;name of reference group pull_group0 = GOLD pull_group1 = CIT pull_group2 = CIT1 pull_group3 = CIT2 pull_group4 = CIT3 pull_group5 = CIT4 pull_group6 = CIT5 pull_group7 = CIT6 pull_group8 = CIT7 pull_group9 = CIT8 pull_group10= CIT9 pull_group11= CIT10 pull_group12= CIT11 ;reference distance at t=0 (nm) pull_rate1 = 0 pull_rate2 = 0 pull_rate3 = 0 pull_rate4 = 0 pull_rate5 = 0 pull_rate6 = 0 pull_rate7 = 0 pull_rate8 = 0 pull_rate9 = 0 pull_rate10 = 0 pull_rate11 = 0 pull_rate12 = 0 However, when I look at the output only the first pull group (CIT) is being restrained at a constant com height from GOLD. The others move away. output from pullx.xvg: 0.0400 0.7177730.9841860.9776820.979256 0.9759620.9787390.9742550.9699420.97706 0.9876681.00157 0.9798940.982414 0.0500 0.7177760.9854420.9771410.979625 0.9760020.9781580.9735630.9685780.97746 0.9890671.00363 0.9800260.983273 0.0600 0.7177760.9867090.9766050.980068 0.9760340.9776710.9730370.9678930.977855 0.9903711.00531 0.9801480.984034 0.0700 0.7177760.9879650.9762220.98048 0.976129 0.9772310.9726260.9675350.9782390.991569 1.00703 0.9802980.984731 0.0800 0.7177760.9891290.9760230.980946 0.9762850.9767170.9722570.9671840.978667 0.99272 1.0089 0.9805040.985445 0.0900 0.7177760.9901860.97597 0.98157 0.976445 0.9762520.9718880.9668410.97909 0.9939441.01091 0.9807840.986181 0.1000 0.7177760.9911790.9760240.9822750.9766 0.9758470.9714450.9665490.9794370.995328 1.01311 0.98115 0.986935 0.1100 0.7177760.9921670.9761650.982984 0.9767870.9753440.9708580.9662750.979715 0.9969571.01556 0.9816190.987732 I was wondering what I have done wrong in the input .mdp file. From looking at the manual, I can't work it out since I think I have set it up as shown. Thanks in advance Louise -- 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] g_analyze doubt
Dear Gromacs Users, i have data for the distance between the protein and water atoms within a cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze on this data. The time frame in the output data is not continuous because of the cut off provided. So i would like to know how would the g_analyze would compute the data. Thanks -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- 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] H-bonds
Hi everyone! I tried doing H-bond analysis using g_hbond on a solute dissolved in water. The solute has hydroxyl groups. In an attempt to analyze water-bridges formed thru H-bonds, I noticed that g_hbond does not seem to give consistent results. As previously discussed in this list, I am taking advantage of the hbmap file to parse out the Hbond trajectories needed to count the water bridges. A possible water-bridge type is one in which the hydrogen of a water molecule is shared by two different oxygens of the solute. Since there are two H's per water molecule I expected two sets of indices for each H. This is what I did. 1. To simplify parsing the resulting HBMap, I intended to create an HBMap.xpm for a water and a pair of hydroxyl residues from the solute. For a shared H above, that would be (O solute...Hwater...O solute). Creating a set of indices for this configuration was successful upon running (g_hbond -hbn), but only for one set of Hwater. g_hbond was not able to create another set for the other H of water. (Note though that g_hbond was able to correctly identify both Hs of water as donors). g_hbond correctly counted H-bonds for this set and produced a reliable HBMap.xpm 2. Another set of indices was manually created for the other H. However, the hbnum.xvg of this set is unreliable compared with the above and the values shoot to 1000 times expected h-bond counts. Please note that the HBMap.xpm for the hydrogen bonds between water and the solute only lists one H for each water as if ignoring the other H (in cases that there should be two). Your advice/ideas/comments is very much welcome and very much needed. Thanks, Bernard -- 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] problem with make_ndx
You should first make an *.itp file for DPPC, then include it in the *.top file. whatever that is not in GROMACS library should be defined to it. You would better see http://davapc1.bioch.dundee.ac.uk/prodrg/gmx.pdf , hope it will help. From: Anushree Tripathi anushritripa...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, February 1, 2012 10:34 AM Subject: [gmx-users] problem with make_ndx When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is showing the following options: 0 System : 18379 atoms 1 Protein : 11739 atoms 2 Protein-H : 9135 atoms 3 C-alpha : 1173 atoms 4 Backbone : 3519 atoms 5 MainChain : 4693 atoms 6 MainChain+Cb : 5773 atoms 7 MainChain+H : 5842 atoms 8 SideChain : 5897 atoms 9 SideChain-H : 4442 atoms 10 Prot-Masses : 11739 atoms 11 non-Protein : 6640 atoms 12 Water : 6636 atoms 13 SOL : 6636 atoms 14 non-Water : 11743 atoms 15 Ion : 4 atoms 16 CL : 4 atoms 17 Water_and_ions : 6640 atoms for my work, I used 16|13 then 1|11.lastly I saved it using 'q'.But there is no option for DPPC (as given in tutorial we have to merge protein with DPPC).After runing the command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),it is showing error: Group DPPC not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. To troubleshoot the error,I have kept one more group in index.ndx file with number of atoms which I found from dppc.itp file(at the end of file) like this [DPPC] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 Again after running the grompp command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),I am getting the following error: Atom 1 in multiple T-Coupling groups (1 and 2). Please suggest me the reason as well as solution for this problem. -- 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
Re: [gmx-users] problem with make_ndx
Anushree Tripathi wrote: But in coordinate file(.pdb file) ,I am not getting the atoms which belongs to DPPC.only I have included the name of dppc.itp file like this: This is precisely the problem - you have no DPPC in the coordinate file. ;Include DPPC chain topology #include dppc.itp Adding information to the topology has no effect on the coordinate file. Consult the membrane protein tutorial for how to properly build such a system. http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations -Justin That's why I have found the atoms wich belongs to DPPC molecule from dppc.itp file itself. On Wed, Feb 1, 2012 at 12:40 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 1/02/2012 6:04 PM, Anushree Tripathi wrote: When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is showing the following options: 0 System : 18379 atoms 1 Protein : 11739 atoms 2 Protein-H : 9135 atoms 3 C-alpha : 1173 atoms 4 Backbone: 3519 atoms 5 MainChain : 4693 atoms 6 MainChain+Cb: 5773 atoms 7 MainChain+H : 5842 atoms 8 SideChain : 5897 atoms 9 SideChain-H : 4442 atoms 10 Prot-Masses : 11739 atoms 11 non-Protein : 6640 atoms 12 Water : 6636 atoms 13 SOL : 6636 atoms 14 non-Water : 11743 atoms 15 Ion : 4 atoms 16 CL : 4 atoms 17 Water_and_ions : 6640 atoms So your system has 18K atoms, with 11K protein and the rest solvent and ions. As Justin suggested, this coordinate file does not have DPPC in it. for my work, I used 16|13 then 1|11.lastly I saved it using 'q'.But there is no option for DPPC (as given in tutorial we have to merge protein with DPPC).After runing the command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),it is showing error: Group DPPC not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. To troubleshoot the error,I have kept one more group in index.ndx file with number of atoms which I found from dppc.itp file(at the end of file) like this [DPPC] 123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 These numbers have to reference the atom numbers in the coordinate file, not the [moleculetype]. Since you've done the latter, you get the problem with T-coupling groups. But go back and use a coordinate file that actually has DPPC in it. Mark Again after running the grompp command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),I am getting the following error: Atom 1 in multiple T-Coupling groups (1 and 2). Please suggest me the reason as well as solution for this problem. -- gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] problem with make_ndx
On 1/02/2012 6:25 PM, Anushree Tripathi wrote: But in coordinate file(.pdb file) ,I am not getting the atoms which belongs to DPPC. You cannot do anything unless you have a coordinate file that includes DPPC coordinates. I don't know how to express this any more clearly. only I have included the name of dppc.itp file like this: ;Include DPPC chain topology #include dppc.itp That's why I have found the atoms wich belongs to DPPC molecule from dppc.itp file itself. These numbers are not useful, as I have already explained. Mark On Wed, Feb 1, 2012 at 12:40 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 1/02/2012 6:04 PM, Anushree Tripathi wrote: When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is showing the following options: 0 System : 18379 atoms 1 Protein : 11739 atoms 2 Protein-H : 9135 atoms 3 C-alpha : 1173 atoms 4 Backbone: 3519 atoms 5 MainChain : 4693 atoms 6 MainChain+Cb: 5773 atoms 7 MainChain+H : 5842 atoms 8 SideChain : 5897 atoms 9 SideChain-H : 4442 atoms 10 Prot-Masses : 11739 atoms 11 non-Protein : 6640 atoms 12 Water : 6636 atoms 13 SOL : 6636 atoms 14 non-Water : 11743 atoms 15 Ion : 4 atoms 16 CL : 4 atoms 17 Water_and_ions : 6640 atoms So your system has 18K atoms, with 11K protein and the rest solvent and ions. As Justin suggested, this coordinate file does not have DPPC in it. for my work, I used 16|13 then 1|11.lastly I saved it using 'q'.But there is no option for DPPC (as given in tutorial we have to merge protein with DPPC).After runing the command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),it is showing error: Group DPPC not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. To troubleshoot the error,I have kept one more group in index.ndx file with number of atoms which I found from dppc.itp file(at the end of file) like this [DPPC] 123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 These numbers have to reference the atom numbers in the coordinate file, not the [moleculetype]. Since you've done the latter, you get the problem with T-coupling groups. But go back and use a coordinate file that actually has DPPC in it. Mark Again after running the grompp command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),I am getting the following error: Atom 1 in multiple T-Coupling groups (1 and 2). Please suggest me the reason as well as solution for this problem. -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_dist
dina dusti wrote: Dear Prof. Thank you very much from your response. Yes, dist.xvg has four column consists origin distance and distances in direction x, y , z. So distance that I want according to result of g_analyze, is 5.324286e-02 that isn't correct. I selected 2 groups, micelle and the last carbon bounded with head group for index file. Also, I did this job for micelle and head group, and micelle with other groups but my results (distances) were all of them near the zero. Please help me to obtain correct distance. Keep in mind what g_dist is measuring, center-of-mass distances. If you select the micelle headgroups and then terminal carbon atoms, the positions will be almost coincident, as your result suggests. Other groups that are giving a nearly-zero distance are likely coincident in the same manner. -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] the DNA md simulation
Dear all; Through the MD simulation for a DNA, I wonder whether we should change any options for the terminal bases or not. Thank you in advance B.Mehrazma -- 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] Pulling multiple groups
Wright, Louise wrote: Hi I am trying to use the pull code of gromacs (version 4.5.5) to constrain the com of a number of groups (labelled CIT, CIT1, CIT2...) to a reference group (labelled GOLD). This is the segment of the .mdp file I have used: ;CoM pull calculations pull= constraint pull_geometry = distance pull_dim= N N Y pull_constr_tol = 1e-6 ; add COM distance of starting config to pull_init pull_start = yes ;frequency for writing COMS of all pull group pull_nstxout= 10 ;frequency for writing force of all pull group pull_nstfout= 10 pull_ngroups= 12 ;name of reference group pull_group0 = GOLD pull_group1 = CIT pull_group2 = CIT1 pull_group3 = CIT2 pull_group4 = CIT3 pull_group5 = CIT4 pull_group6 = CIT5 pull_group7 = CIT6 pull_group8 = CIT7 pull_group9 = CIT8 pull_group10= CIT9 pull_group11= CIT10 pull_group12= CIT11 ;reference distance at t=0 (nm) pull_rate1 = 0 pull_rate2 = 0 pull_rate3 = 0 pull_rate4 = 0 pull_rate5 = 0 pull_rate6 = 0 pull_rate7 = 0 pull_rate8 = 0 pull_rate9 = 0 pull_rate10 = 0 pull_rate11 = 0 pull_rate12 = 0 However, when I look at the output only the first pull group (CIT) is being restrained at a constant com height from GOLD. The others move away. output from pullx.xvg: 0.0400 0.7177730.9841860.9776820.979256 0.9759620.9787390.9742550.9699420.97706 0.9876681.00157 0.9798940.982414 0.0500 0.7177760.9854420.9771410.979625 0.9760020.9781580.9735630.9685780.97746 0.9890671.00363 0.9800260.983273 0.0600 0.7177760.9867090.9766050.980068 0.9760340.9776710.9730370.967893 0.9778550.9903711.00531 0.9801480.984034 0.0700 0.7177760.9879650.9762220.98048 0.9761290.9772310.9726260.967535 0.9782390.9915691.00703 0.9802980.984731 0.0800 0.7177760.9891290.9760230.980946 0.9762850.9767170.9722570.967184 0.9786670.99272 1.0089 0.9805040.985445 0.0900 0.7177760.9901860.97597 0.98157 0.976445 0.9762520.9718880.9668410.97909 0.993944 1.01091 0.9807840.986181 0.1000 0.7177760.9911790.9760240.982275 0.9766 0.9758470.9714450.9665490.979437 0.9953281.01311 0.98115 0.986935 0.1100 0.7177760.9921670.9761650.982984 0.9767870.9753440.9708580.966275 0.9797150.9969571.01556 0.9816190.987732 I was wondering what I have done wrong in the input .mdp file. From looking at the manual, I can't work it out since I think I have set it up as shown. Do the distances continually get larger? I see no clear evidence of that here, but it is a short timeframe. The COM separation will fluctuate to a small extent; you should not expect the distance to remain absolutely fixed. -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] g_analyze doubt
aiswarya pawar wrote: Dear Gromacs Users, i have data for the distance between the protein and water atoms within a cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze on this data. The time frame in the output data is not continuous because of the cut off provided. So i would like to know how would the g_analyze would compute the data. I'm not clear on what you're trying to do. g_analyze performs simple statistical operations (averages, error estimates) on the input data. If there are discontinuities (which I do not understand the nature of), they come from the g_dist data, not what g_analyze is doing. Please provide a more clear description of what you are doing, including all relevant commands, and examples of the data files, 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
Re: [gmx-users] the DNA md simulation
Banafsheh Mehrazma wrote: Dear all; Through the MD simulation for a DNA, I wonder whether we should change any options for the terminal bases or not. What is it that you think you should change? -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] g_analyze doubt
Hi, I have used the command = g_dist -f md.xtc -s md.tpr -n index.ndx which gives an output of data= 0.0000.62590240.3880.3610001 -0.3329997 1.0000.67787750.25900030.593 -0.198 2.0000.67590300.25299980.593 -0.203 3.0000.64633530.16900010.5680003 -0.257 4.0000.68088910.2630.605 -0.1669998 5.0000.68835610.3090.592 -0.1670003 6.0000.62016600.27699970.513 -0.2090001 7.0000.68320050.29100010.580 -0.211 8.0000.64729990.29600020.533 -0.2150002 9.0000.65426920.1880.540 -0.3180003 10.0000.67256020.32300020.5780001 -0.118 11.0000.61387120.34700010.4769998 -0.171 12.0000.69996450.2860.6150002 -0.172 13.0000.65045930.1210.6160002 -0.171 14.0000.64471600.2110.586 -0.1629996 15.0000.66456100.2040.5710001 -0.2720003 16.0000.64812760.23300030.5560002 -0.237 17.0000.6530.22400020.560 -0.243 18.0000.71192580.26500010.6220002 -0.223 19.0000.66535630.0920.6170001 -0.230 20.0000.68816380.25200010.6070004 -0.204 21.0000.71619440.20900010.6220002 -0.2870002 22.0000.65877780.1410.6020002 -0.2279997 23.0000.57986310.01700020.5160003 -0.263 24.0000.58625640.0390.5239997 -0.258 25.0000.6923014 -0.12400010.552 -0.3990002 26.0000.5787479 -0.0870.5050001 -0.2680001 27.0000.5776323 -0.25899980.473 -0.2070003 28.0000.5910018 -0.16300010.5250001 -0.217 29.0000.4448786 -0.15700010.402 -0.1079998 30.0000.4806164 -0.21600010.401 -0.1560001 31.0000.5405830 -0.1710.473 -0.198 32.0000.5614526 -0.10800030.493 -0.2459998 33.0000.4994450 -0.0730.453 -0.204 34.0000.5323368 -0.14200020.4830003 -0.1730003 From this the first column is the time and the second is the water protein atom distance. so when am using the g_analyze i would use the 1st and 2nd column for the input? More over now this distances are below 0.8 nm . what would i do if my data in between shows distance more than 0.8nm. Thanks On Wed, Feb 1, 2012 at 6:48 PM, Justin A. Lemkul jalem...@vt.edu wrote: aiswarya pawar wrote: Dear Gromacs Users, i have data for the distance between the protein and water atoms within a cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze on this data. The time frame in the output data is not continuous because of the cut off provided. So i would like to know how would the g_analyze would compute the data. I'm not clear on what you're trying to do. g_analyze performs simple statistical operations (averages, error estimates) on the input data. If there are discontinuities (which I do not understand the nature of), they come from the g_dist data, not what g_analyze is doing. Please provide a more clear description of what you are doing, including all relevant commands, and examples of the data files, 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore -- 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] g_analyze doubt
On 2/02/2012 12:28 AM, aiswarya pawar wrote: Hi, I have used the command = g_dist -f md.xtc -s md.tpr -n index.ndx which gives an output of data= 0.0000.62590240.3880.3610001 -0.3329997 1.0000.67787750.25900030.593 -0.198 2.0000.67590300.25299980.593 -0.203 3.0000.64633530.16900010.5680003 -0.257 4.0000.68088910.2630.605 -0.1669998 5.0000.68835610.3090.592 -0.1670003 6.0000.62016600.27699970.513 -0.2090001 7.0000.68320050.29100010.580 -0.211 8.0000.64729990.29600020.533 -0.2150002 9.0000.65426920.1880.540 -0.3180003 10.0000.67256020.32300020.5780001 -0.118 11.0000.61387120.34700010.4769998 -0.171 12.0000.69996450.2860.6150002 -0.172 13.0000.65045930.1210.6160002 -0.171 14.0000.64471600.2110.586 -0.1629996 15.0000.66456100.2040.5710001 -0.2720003 16.0000.64812760.23300030.5560002 -0.237 17.0000.6530.22400020.560 -0.243 18.0000.71192580.26500010.6220002 -0.223 19.0000.66535630.0920.6170001 -0.230 20.0000.68816380.25200010.6070004 -0.204 21.0000.71619440.20900010.6220002 -0.2870002 22.0000.65877780.1410.6020002 -0.2279997 23.0000.57986310.01700020.5160003 -0.263 24.0000.58625640.0390.5239997 -0.258 25.0000.6923014 -0.12400010.552 -0.3990002 26.0000.5787479 -0.0870.5050001 -0.2680001 27.0000.5776323 -0.25899980.473 -0.2070003 28.0000.5910018 -0.16300010.5250001 -0.217 29.0000.4448786 -0.15700010.402 -0.1079998 30.0000.4806164 -0.21600010.401 -0.1560001 31.0000.5405830 -0.1710.473 -0.198 32.0000.5614526 -0.10800030.493 -0.2459998 33.0000.4994450 -0.0730.453 -0.204 34.0000.5323368 -0.14200020.4830003 -0.1730003 From this the first column is the time and the second is the water protein atom distance. so when am using the g_analyze i would use the 1st and 2nd column for the input? More over now this distances are below 0.8 nm . what would i do if my data in between shows distance more than 0.8nm. The above command measures distances between centres of masses of groups, like g_dist -h says. It doesn't measure distance between protein and water atoms within a cut off. You still haven't described what you're trying to measure, or what your simulation looks like, so it's impossible to help you. Mark Thanks On Wed, Feb 1, 2012 at 6:48 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: aiswarya pawar wrote: Dear Gromacs Users, i have data for the distance between the protein and water atoms within a cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze on this data. The time frame in the output data is not continuous because of the cut off provided. So i would like to know how would the g_analyze would compute the data. I'm not clear on what you're trying to do. g_analyze performs simple statistical operations (averages, error estimates) on the input data. If there are discontinuities (which I do not understand the nature of), they come from the g_dist data, not what g_analyze is doing. Please provide a more clear description of what you are doing, including all relevant commands, and examples of the data files, 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 http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science
Re: [gmx-users] g_analyze doubt
aiswarya pawar wrote: Hi, I have used the command = g_dist -f md.xtc -s md.tpr -n index.ndx which gives an output of data= 0.0000.62590240.3880.3610001 -0.3329997 1.0000.67787750.25900030.593 -0.198 2.0000.67590300.25299980.593 -0.203 3.0000.64633530.16900010.5680003 -0.257 4.0000.68088910.2630.605 -0.1669998 5.0000.68835610.3090.592 -0.1670003 6.0000.62016600.27699970.513 -0.2090001 7.0000.68320050.29100010.580 -0.211 8.0000.64729990.29600020.533 -0.2150002 9.0000.65426920.1880.540 -0.3180003 10.0000.67256020.32300020.5780001 -0.118 11.0000.61387120.34700010.4769998 -0.171 12.0000.69996450.2860.6150002 -0.172 13.0000.65045930.1210.6160002 -0.171 14.0000.64471600.2110.586 -0.1629996 15.0000.66456100.2040.5710001 -0.2720003 16.0000.64812760.23300030.5560002 -0.237 17.0000.6530.22400020.560 -0.243 18.0000.71192580.26500010.6220002 -0.223 19.0000.66535630.0920.6170001 -0.230 20.0000.68816380.25200010.6070004 -0.204 21.0000.71619440.20900010.6220002 -0.2870002 22.0000.65877780.1410.6020002 -0.2279997 23.0000.57986310.01700020.5160003 -0.263 24.0000.58625640.0390.5239997 -0.258 25.0000.6923014 -0.12400010.552 -0.3990002 26.0000.5787479 -0.0870.5050001 -0.2680001 27.0000.5776323 -0.25899980.473 -0.2070003 28.0000.5910018 -0.16300010.5250001 -0.217 29.0000.4448786 -0.15700010.402 -0.1079998 30.0000.4806164 -0.21600010.401 -0.1560001 31.0000.5405830 -0.1710.473 -0.198 32.0000.5614526 -0.10800030.493 -0.2459998 33.0000.4994450 -0.0730.453 -0.204 34.0000.5323368 -0.14200020.4830003 -0.1730003 From this the first column is the time and the second is the water protein atom distance. so when am using the g_analyze i would use the 1st and 2nd column for the input? More over now this distances are below Pass this file directly to g_analyze - there's no need for manipulation. You'll get averages of all four distance columns, but of course just take what you need. 0.8 nm . what would i do if my data in between shows distance more than 0.8nm. You said you had g_dist measure distances between protein atoms and the COM of water molecules within 0.8 nm, so I don't see how a distance greater than 0.8 nm is even possible in this case. -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] Pulling multiple groups
Hi Justin, thanks for your reply. Yes the distances get a lot larger and are definitely not just fluctuating. It is hard to demonstrate this without showing you the whole file which is huge. However, I have used the same input files with gromacs 4.5.4 just now and it works- I think it might be a bug with gromacs 4.5.5 ? Louise -- 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] Pulling multiple groups
Wright, Louise wrote: Hi Justin, thanks for your reply. Yes the distances get a lot larger and are definitely not just fluctuating. It is hard to demonstrate this without showing you the whole file which is huge. However, I have used the same input files with gromacs 4.5.4 just now and it works- I think it might be a bug with gromacs 4.5.5 ? If the problem is reproducible in 4.5.5 but absent in 4.5.4, please file a bug report on redmine.gromacs.org with a .tpr file that produces the problem so that it can be fixed. -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] g_analyze doubt
If i give command as = g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8 this prints out all the protein water distance within 0.8nm. The data printed out is such that= t: 1466 5369 SOL 20624 OW 0.789894 (nm) t: 1467 5369 SOL 20624 OW 0.781596 (nm) t: 1469 5369 SOL 20624 OW 0.785377 (nm) t: 1473 5369 SOL 20624 OW 0.763485 (nm) t: 1474 5369 SOL 20624 OW 0.767805 (nm) t: 1475 5369 SOL 20624 OW 0.736003 (nm) t: 1476 5369 SOL 20624 OW 0.707953 (nm) t: 1477 5369 SOL 20624 OW 0.713135 (nm) t: 1478 5369 SOL 20624 OW 0.694042 (nm) t: 1480 5369 SOL 20624 OW 0.733907 (nm) t: 1481 5369 SOL 20624 OW 0.705245 (nm) t: 1482 5369 SOL 20624 OW 0.678473 (nm) t: 1483 5369 SOL 20624 OW 0.6288 (nm) t: 1492 5369 SOL 20624 OW 0.794252 (nm) t: 1496 5369 SOL 20624 OW 0.753049 (nm) t: 1497 5369 SOL 20624 OW 0.782796 (nm) t: 1498 5369 SOL 20624 OW 0.799607 (nm) t: 1499 5369 SOL 20624 OW 0.69987 (nm) t: 1500 5369 SOL 20624 OW 0.763511 (nm) t: 1501 5369 SOL 20624 OW 0.764072 (nm) t: 1502 5369 SOL 20624 OW 0.739181 (nm) t: 1503 5369 SOL 20624 OW 0.70336 (nm) In the above data can be seen that the time frame is not continuos. i.e. only the time at which the protein water distance within 0.8nm are shown. So is it possible to do g_analyze on this? On 01-Feb-2012, at 6:48 PM, Justin A. Lemkul wrote: aiswarya pawar wrote: Dear Gromacs Users, i have data for the distance between the protein and water atoms within a cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze on this data. The time frame in the output data is not continuous because of the cut off provided. So i would like to know how would the g_analyze would compute the data. I'm not clear on what you're trying to do. g_analyze performs simple statistical operations (averages, error estimates) on the input data. If there are discontinuities (which I do not understand the nature of), they come from the g_dist data, not what g_analyze is doing. Please provide a more clear description of what you are doing, including all relevant commands, and examples of the data files, 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 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] g_analyze doubt
aiswarya pawar wrote: If i give command as = g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8 this prints out all the protein water distance within 0.8nm. The data printed out is such that= t: 1466 5369 SOL 20624 OW 0.789894 (nm) t: 1467 5369 SOL 20624 OW 0.781596 (nm) t: 1469 5369 SOL 20624 OW 0.785377 (nm) t: 1473 5369 SOL 20624 OW 0.763485 (nm) t: 1474 5369 SOL 20624 OW 0.767805 (nm) t: 1475 5369 SOL 20624 OW 0.736003 (nm) t: 1476 5369 SOL 20624 OW 0.707953 (nm) t: 1477 5369 SOL 20624 OW 0.713135 (nm) t: 1478 5369 SOL 20624 OW 0.694042 (nm) t: 1480 5369 SOL 20624 OW 0.733907 (nm) t: 1481 5369 SOL 20624 OW 0.705245 (nm) t: 1482 5369 SOL 20624 OW 0.678473 (nm) t: 1483 5369 SOL 20624 OW 0.6288 (nm) t: 1492 5369 SOL 20624 OW 0.794252 (nm) t: 1496 5369 SOL 20624 OW 0.753049 (nm) t: 1497 5369 SOL 20624 OW 0.782796 (nm) t: 1498 5369 SOL 20624 OW 0.799607 (nm) t: 1499 5369 SOL 20624 OW 0.69987 (nm) t: 1500 5369 SOL 20624 OW 0.763511 (nm) t: 1501 5369 SOL 20624 OW 0.764072 (nm) t: 1502 5369 SOL 20624 OW 0.739181 (nm) t: 1503 5369 SOL 20624 OW 0.70336 (nm) In the above data can be seen that the time frame is not continuos. i.e. only the time at which the protein water distance within 0.8nm are shown. So is it possible to do g_analyze on this? As I said before, g_analyze can only perform statistical operations on the (numerical) data supplied to it. What you've asked g_dist to do is print a list of any atoms that satisfy the distance criteria. You may get frames where there are none, you may get frames where there are several atoms that work. There's nothing here that g_analyze can do anything with. You can't average apples and oranges and hope to get grapes, though you might go bananas :) Sorry, couldn't resist a bit of fun there... -Justin On 01-Feb-2012, at 6:48 PM, Justin A. Lemkul wrote: aiswarya pawar wrote: Dear Gromacs Users, i have data for the distance between the protein and water atoms within a cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze on this data. The time frame in the output data is not continuous because of the cut off provided. So i would like to know how would the g_analyze would compute the data. I'm not clear on what you're trying to do. g_analyze performs simple statistical operations (averages, error estimates) on the input data. If there are discontinuities (which I do not understand the nature of), they come from the g_dist data, not what g_analyze is doing. Please provide a more clear description of what you are doing, including all relevant commands, and examples of the data files, 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 -- 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] Installing GMX-GPU 4.5.5 calculating SASA
So, This is slightly aside from the installation of the openMM (cuda), but is CUDA related. Does anyone know the state of the CUDA to OpenCL porting the AMD (CUDA teams said they were going to do this) and then further all CUDA work as OpenCL, as no one has mentioned anything on this since 2010 (the CUDA web site). There are however several useful code bits such as openCLpython, JAVAopenCL, etc... Also, How much for an ATI emulator that works with CUDA? As I understand it the only main problem is how the 8 by 8 GPU compute units are arranged on the device, and not even the actual code, so one could just easily write the ATI device specs into a CUDA code or vise versa? Just interested but lacking any time to even start to attempt such things, but anything of this nature would make my life and many I know much easier. Sincerely, Stephan Lloyd Watkins Original-Nachricht Datum: Tue, 31 Jan 2012 21:50:53 +0300 Von: Андрей Гончар gontc...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org Betreff: Re: [gmx-users] Installing GMX-GPU 4.5.5 You should try this: http://verahill.blogspot.com/2012/01/debian-testing-64-wheezy-compiling_20.html 2012/1/31 Efrat Exlrod efrat.exl...@biu.ac.il: Hi, I'm compiling gromacs 4.5.5 with gcc compiler (v 4.5.3), cmake (2.8.7) and OpenMM 3.1.1 on Linux (Red Hat release 5.7). I have followed the installation instructions. The configuration seems to work well. ~/progs/cmake-2.8.7/bin/cmake -DGMX_OPENMM=ON -DCUDA_TOOLKIT_ROOT_DIR:PATH=/opt/cuda -DCMAKE_C_COMPILER:FILEPATH=/private/gnss/local/bin/gcc -DCMAKE_INSTALL_PREFIX=/private/gnss/Gromacs_455 But, when I run make mdrun I get the following error: make mdrun [ 0%] Building NVCC (Device) object src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o cc1plus: error: unrecognized command line option -fexcess-precision=fast CMake Error at CMakeFiles/gmx_gpu_utils_generated_memtestG80_core.cu.o.cmake:198 (message): Error generating /private/gnss/Gromacs_Install_455/gromacs-4.5.5/src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o make[3]: *** [src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o] Error 1 make[2]: *** [src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all] Error 2 make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2 make: *** [mdrun] Error 2 When I run make mdrun after deleting the 2 occurences of -fexcess-precision=fast from CMakeCache.txt the compilation works. What could be the problem? Thanks, Efrat -- 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 -- Андрей Гончар -- 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 -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://www.gmx.net/de/go/freephone/ -- 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] segmantation default
hi all... ı have a problem.. ı got segmentation fault when run nvt equilibration.. ı use below mdp file ; Run control integrator = sd ; Langevin dynamics tinit= 0 dt = 0.002 nsteps = 5; 100 ps nstcomm = 100 ; Output control nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxtcout= 0 xtc-precision= 1000 ; Neighborsearching and short-range nonbonded interactions nstlist = 10 ns_type = grid pbc = xyz rlist= 1.5 [ Read 70 lines ] ^G Get Help ^O WriteOut ^R Read File ^Y Prev Page ^K Cut Text ^C Cur Pos ^X Exit ^J Justify ^W Where Is ^V Next Page ^U UnCut Text^T To Spell GNU nano 2.2.2 File: nvt.mdp ; Run control integrator = sd ; Langevin dynamics tinit= 0 dt = 0.002 nsteps = 5; 100 ps nstcomm = 100 ; Output control nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxtcout= 0 xtc-precision= 1000 ; Neighborsearching and short-range nonbonded interactions nstlist = 10 ns_type = grid pbc = xyz rlist= 1.5 [ Read 70 lines ] ^G Get Help ^O WriteOut ^R Read File ^Y Prev Page ^K Cut Text ^C Cur Pos ^X Exit ^J Justify ^W Where Is ^V Next Page ^U UnCut Text^T To Spell GNU nano 2.2.2File: nvt.mdp couple-lambda0 = vdw ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW couple-intramol = no nstdhdl = 10 ; Generate velocities to start gen_vel = yes gen_temp = 300 gen_seed = -1 ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Do not constrain the starting configuration continuation = no ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 and ı received this message.. bombardment on your system Getting Loaded... Reading file nvt.tpr, VERSION 4.5.4 (single precision) Starting 8 threads Loaded with Money Making 2D domain decomposition 4 x 2 x 1 starting mdrun 'Protein in water' 5 steps,100.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.900710, max 1.180984 (between atoms 1 and 4) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1 2 44.90.1000 0.0977 0.1000 1 3 90.00.1000 0.2019 0.1000 1 4 90.00.1000 0.2181 0.1000 Wrote pdb files with previous and current coordinates Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.900025, max 1.179635 (between atoms 1 and 4) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1 2 44.90.1000 0.0977 0.1000 1 3 90.00.1000 0.2019 0.1000 1 4 90.00.1000 0.2180 0.1000 Back Off! I just backed up step0b_n4.pdb to ./#step0b_n4.pdb.1# Back Off! I just backed up step0c_n4.pdb to ./#step0c_n4.pdb.1# Wrote pdb files with previous and current coordinates step 0 Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.078096, max 0.132700 (between atoms 1 and 4) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1 3 47.20.2019 0.0981 0.1000 1 4 90.00.2180 0.1133 0.1000 Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.078081, max 0.132660 (between atoms 1 and 4) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1 3 47.30.2019 0.0981 0.1000 1 4 90.00.2180 0.1133 0.1000 Step 2, time 0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 1.319803, max 2.026278 (between atoms 1 and 4) Step 2, time 0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.349996, max 0.441907 (between atoms 11 and 12) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current,
[gmx-users] Gromacs GPU tutorial at MD workshop
Hi all, The NAIS Centre in Edinburgh is holding a Workshop on State-of-the-Art Algorithms for Molecular Dynamics on May 2-4. The days before this workshop, April 30-May 2, I and David Hardy from NAMD will organize a tutorial on the use of GPUs and parallel computing. Here, among other things, Szilard Pall and I will present the algorithmic details and the performance of the new multi-level heterogeneous parallelization (MPI+OpenMP and GPU) of Gromacs 4.6 which will soon be released. For details and registration go to: http://www.nais.org.uk/MD2012/ Cheers, Berk -- 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] g_dist
Dear Prof. Thank you very much from your response. but I didn't select micelle headgroups and then terminal carbon atom but also I selected COM of micelle and for example head group of micelle! The calulation of radius of micelle by radius of gyration give that is near 2.3-2.4 nm but g_dist ...!!! Where is my mistake? I select groups in index file correctly. Please help me. Thank you again. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, February 1, 2012 3:13 PM Subject: Re: [gmx-users] g_dist dina dusti wrote: Dear Prof. Thank you very much from your response. Yes, dist.xvg has four column consists origin distance and distances in direction x, y , z. So distance that I want according to result of g_analyze, is 5.324286e-02 that isn't correct. I selected 2 groups, micelle and the last carbon bounded with head group for index file. Also, I did this job for micelle and head group, and micelle with other groups but my results (distances) were all of them near the zero. Please help me to obtain correct distance. Keep in mind what g_dist is measuring, center-of-mass distances. If you select the micelle headgroups and then terminal carbon atoms, the positions will be almost coincident, as your result suggests. Other groups that are giving a nearly-zero distance are likely coincident in the same manner. -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] g_rdf
Dear Prof. Thank you very much from your reply. Is your mean that density=(N/V)*g(r), where N is the number of total atoms in box not in the shell and V is the volume of box not in the shell? Best Regards Sara From: Dallas Warren dallas.war...@monash.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, February 1, 2012 2:12 AM Subject: RE: [gmx-users] g_rdf An RDF is normalised to the density for the entire box, so you should simply be using that. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From:gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mohammad agha Sent: Tuesday, 31 January 2012 7:26 PM To: gmx-users@gromacs.org Subject: [gmx-users] g_rdf Dear Prof. I am confused about generation a radial density graph (density vs distance from center of mass), I know that I should use g_rdf. Then I count the number of atoms in the shells around the COM of special group by trjorder -com -nshell -r , next I use from this formula for compute the density: density = (dN/4*pi*dr*r^2)*g(r), where dN, dr, r and g(r) are the number of atoms in each shell, wide of shell, radius of COM of special group, and averaged RDF in each shell, respectively. While the plot of g(r) is consistent with published previous results but density has not consistence with them, I think that I am wrong in compute the density. Please help me. Best Regards Sara -- 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] g_dist
Dear Prof. Thank you very much from your response. I removed pbc and jump in my system, and when I see my system as visual in ngmx, there is not pbc and jump and has been created one micelle and it remain stable for long times. I really don't know what should I do! Best Regards Dina -- 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 analysis tools for Namd output
Dear Gromacs users, I want to use the Gromacs analysis tools for analyzing Namd output files (*.dcd files) I just installed Gromacs 4.5.4 and it works well. In addition I installed VMD 1.9 and set up VMD_PLUGIN_PATH=/home/vmd-1.9/plugins/LINUXAMD64/molfile/ (Here it is located the dcdplugin.so ) I verified that VMD_PLUGIN_PATH is pointing out to the right folder. However when I run for example g_rmsf_d -f file.dcd -s file.pdb I got the following error The file format of file.dcd is not a known trajectory format to GROMACS. Please make sure that the file is a trajectory! GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins. This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD. No plugin for dcd found Am I doing something wrong? Do I need to do something else? Any help and advise will be highly appreciate it -- Cheers, Paul -- 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] segmantation default
mehmet kıytak wrote: hi all... ı have a problem.. ı got segmentation fault when run nvt equilibration.. ı use below mdp file Please post a complete .mdp file. The Unix 'cat' command can be used to print the contents of the text file, which can then be copied and pasted into an email. couple-lambda0 = vdw ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW couple-intramol = no nstdhdl = 10 It appears you are trying to do a free energy calculation by transforming your system. Turn off the free energy code to determine whether or not this is a source of the problem. snip Step 3, time 0.006 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.337002, max 0.559171 (between atoms 1 and 4) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1 2 90.00.1006 0.1091 0.1000 1 3 90.00.2058 0.1141 0.1000 1 4 90.00.3028 0.1559 0.1000 Back Off! I just backed up step3b_n3.pdb to ./#step3b_n3.pdb.1# Back Off! I just backed up step3b_n4.pdb to ./#step3b_n4.pdb.1# Back Off! I just backed up step3c_n2.pdb to ./#step3c_n2.pdb.1# Back Off! I just backed up step3c_n3.pdb to ./#step3c_n3.pdb.1# Back Off! I just backed up step3c_n4.pdb to ./#step3c_n4.pdb.1# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Segmentation fault mkiytak@babil:~ PLEASE HELP ME... LINCS warnings are the most common error reported to this list. Please refer to the following pages for help: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings If you still can't find your answer, refer to the list archive. As I said, such errors are commonly reported. Surely you'll find something useful. The only thing that can be said right now is that your system is unstable. Either you need better minimization or equilibration (or both), your .mdp settings are incorrect, or the free energy code is causing an instability (which is a symptom of the first two points, it does not suggest the free energy code is not working). -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] g_dist
dina dusti wrote: Dear Prof. Thank you very much from your response. but I didn't select micelle headgroups and then terminal carbon atom but also I selected COM of micelle and for example head group of micelle! The calulation of radius of micelle by radius of gyration give that is near 2.3-2.4 nm but g_dist ...!!! g_dist and g_gyrate work in different ways. You can't equate their output. A micelle is (roughly) a sphere. The COM of the headgroups will be the center of the sphere. Thus, the COM of the micelle is the COM of the sphere and the COM of the headgroups is (approximately) coincident. Hence why you are getting a very tiny distance reported by g_dist. Where is my mistake? I select groups in index file correctly. Please help me. g_rdf might be a better option, by selecting the COM of the micelle as the reference and the headgroups as the group for calculation. That way you will get the distribution of headgroup distances from the COM of the micelle, thus approximately the radius of the micelle. -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] g_dist
Dear Prof. Thank you very much for your help. Yes, I also used from g_rdf and g_gyrate but I am seeking root-mean-square distance that there is in many articles for calculation of radius of micelle and radius of dry core (hydrocarbone). I understood that they used g_dist but it doesn't work me. Perhaps I am wrong about required program (command) for calculation of root-mean-square distance? Please help me. Thank you again. Best Regards Dina From: Justin A. Lemkul jalem...@vt.edu To: dina dusti dinadu...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, February 1, 2012 9:15 PM Subject: Re: [gmx-users] g_dist dina dusti wrote: Dear Prof. Thank you very much from your response. but I didn't select micelle headgroups and then terminal carbon atom but also I selected COM of micelle and for example head group of micelle! The calulation of radius of micelle by radius of gyration give that is near 2.3-2.4 nm but g_dist ...!!! g_dist and g_gyrate work in different ways. You can't equate their output. A micelle is (roughly) a sphere. The COM of the headgroups will be the center of the sphere. Thus, the COM of the micelle is the COM of the sphere and the COM of the headgroups is (approximately) coincident. Hence why you are getting a very tiny distance reported by g_dist. Where is my mistake? I select groups in index file correctly. Please help me. g_rdf might be a better option, by selecting the COM of the micelle as the reference and the headgroups as the group for calculation. That way you will get the distribution of headgroup distances from the COM of the micelle, thus approximately the radius of the micelle. -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] g_dist
dina dusti wrote: Dear Prof. Thank you very much for your help. Yes, I also used from g_rdf and g_gyrate but I am seeking root-mean-square distance that there is in many articles for calculation of radius of micelle and radius of dry core (hydrocarbone). I understood that they used g_dist but it doesn't work me. Perhaps I am wrong about required program (command) for calculation of root-mean-square distance? Didn't Tsjerk already answer this? http://lists.gromacs.org/pipermail/gmx-users/2012-January/067984.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] g_dist
Dear Prof. Thank you very much from your response. He answer me that I should use from g_gyration for radius of micelle, but what should I do for hydrocarbon (dry) core or calculation of inner core of micelle (i.e. the first of carbon on tail of surfactant with COM of micelle)? Best Regards Dina -- 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] segmantation default
hi justin ı used this mdp. file ..simulation box may be wrong.?..ı used dodecahedron distance edge 2.0 nm. ; Run control integrator = sd ; Langevin dynamics tinit= 0 dt = 0.002 nsteps = 250 ; 5 ns nstcomm = 100 ; Output control nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 0 nstenergy= 0 nstxtcout= 0 xtc-precision= 1000 ; Neighborsearching and short-range nonbonded interactions nstlist = 10 ns_type = grid pbc = xyz rlist= 1.0 ; Electrostatics coulombtype = PME rcoulomb = 1.0 ; van der Waals vdw-type = switch rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tc_grps = system tau_t= 1.0 ref_t= 300 ; Pressure coupling is on for NPT Pcoupl = Parrinello-Rahman tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 couple-moltype = system ; name of moleculetype to decouple couple-lambda0 = vdw ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW couple-intramol = no nstdhdl = 10 ; Do not generate velocities gen_vel = no ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Constrain the starting configuration ; since we are continuing from NPT continuation = yes ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 1 Şubat 2012 19:41 tarihinde Justin A. Lemkul jalem...@vt.edu yazdı: mehmet kıytak wrote: hi all... ı have a problem.. ı got segmentation fault when run nvt equilibration.. ı use below mdp file Please post a complete .mdp file. The Unix 'cat' command can be used to print the contents of the text file, which can then be copied and pasted into an email. couple-lambda0 = vdw ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW couple-intramol = no nstdhdl = 10 It appears you are trying to do a free energy calculation by transforming your system. Turn off the free energy code to determine whether or not this is a source of the problem. snip Step 3, time 0.006 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.337002, max 0.559171 (between atoms 1 and 4) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1 2 90.00.1006 0.1091 0.1000 1 3 90.00.2058 0.1141 0.1000 1 4 90.00.3028 0.1559 0.1000 Back Off! I just backed up step3b_n3.pdb to ./#step3b_n3.pdb.1# Back Off! I just backed up step3b_n4.pdb to ./#step3b_n4.pdb.1# Back Off! I just backed up step3c_n2.pdb to ./#step3c_n2.pdb.1# Back Off! I just backed up step3c_n3.pdb to ./#step3c_n3.pdb.1# Back Off! I just backed up step3c_n4.pdb to ./#step3c_n4.pdb.1# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Segmentation fault mkiytak@babil:~ PLEASE HELP ME... LINCS warnings are the most common error reported to this list. Please refer to the following pages for help: http://www.gromacs.org/**Documentation/Errors#LINCS.** 2fSETTLE.2fSHAKE_warningshttp://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings If you still can't find your answer, refer to the list archive. As I said, such errors are commonly reported. Surely you'll find something useful. The only thing that can be said right now is that your system is unstable. Either you need better minimization or equilibration (or both), your .mdp settings are incorrect, or the free energy code is causing an instability (which is a symptom of the first two points, it does not suggest the free energy code is
Re: [gmx-users] segmantation default
mehmet kıytak wrote: hi justin ı used this mdp. file ..simulation box may be wrong.?..ı used dodecahedron distance edge 2.0 nm. No, that's almost certainly not the problem. Insufficient minimization/equilibration, or instability due to the use of the free energy code is more likely. You look to be trying to decouple the entire system, which could be an unstable process. You haven't said what you're doing, so I won't hazard a guess at this point. Please refer to the link I provided and try running without the free energy code. Otherwise, you're (potentially) trying to solve several problems at once. -Justin ; Run control integrator = sd ; Langevin dynamics tinit= 0 dt = 0.002 nsteps = 250 ; 5 ns nstcomm = 100 ; Output control nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 0 nstenergy= 0 nstxtcout= 0 xtc-precision= 1000 ; Neighborsearching and short-range nonbonded interactions nstlist = 10 ns_type = grid pbc = xyz rlist= 1.0 ; Electrostatics coulombtype = PME rcoulomb = 1.0 ; van der Waals vdw-type = switch rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; EWALD/PME/PPPM parameters pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Temperature coupling ; tcoupl is implicitly handled by the sd integrator tc_grps = system tau_t= 1.0 ref_t= 300 ; Pressure coupling is on for NPT Pcoupl = Parrinello-Rahman tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; Free energy control stuff free_energy = yes init_lambda = 0.0 delta_lambda = 0 foreign_lambda = 0.05 sc-alpha = 0.5 sc-power = 1.0 sc-sigma = 0.3 couple-moltype = system ; name of moleculetype to decouple couple-lambda0 = vdw ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW couple-intramol = no nstdhdl = 10 ; Do not generate velocities gen_vel = no ; options for bonds constraints = h-bonds ; we only have C-H bonds here ; Type of constraint algorithm constraint-algorithm = lincs ; Constrain the starting configuration ; since we are continuing from NPT continuation = yes ; Highest order in the expansion of the constraint coupling matrix lincs-order = 12 1 Şubat 2012 19:41 tarihinde Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu yazdı: mehmet kıytak wrote: hi all... ı have a problem.. ı got segmentation fault when run nvt equilibration.. ı use below mdp file Please post a complete .mdp file. The Unix 'cat' command can be used to print the contents of the text file, which can then be copied and pasted into an email. couple-lambda0 = vdw ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW couple-intramol = no nstdhdl = 10 It appears you are trying to do a free energy calculation by transforming your system. Turn off the free energy code to determine whether or not this is a source of the problem. snip Step 3, time 0.006 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.337002, max 0.559171 (between atoms 1 and 4) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1 2 90.00.1006 0.1091 0.1000 1 3 90.00.2058 0.1141 0.1000 1 4 90.00.3028 0.1559 0.1000 Back Off! I just backed up step3b_n3.pdb to ./#step3b_n3.pdb.1# Back Off! I just backed up step3b_n4.pdb to ./#step3b_n4.pdb.1# Back Off! I just backed up step3c_n2.pdb to ./#step3c_n2.pdb.1# Back Off! I just backed up step3c_n3.pdb to ./#step3c_n3.pdb.1# Back Off! I just backed up step3c_n4.pdb to ./#step3c_n4.pdb.1# Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates Segmentation fault
Re: [gmx-users] g_dist
dina dusti wrote: Dear Prof. Thank you very much from your response. He answer me that I should use from g_gyration for radius of micelle, but what should I do for hydrocarbon (dry) core or calculation of inner core of micelle (i.e. the first of carbon on tail of surfactant with COM of micelle)? Use g_gyrate, with a custom index group that contains the atoms of interest. If you're interested in the radius of the hydrocarbon atoms, make that an index group and perform the analysis on it. -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] g_analyze doubt
On 2/02/2012 2:08 AM, aiswarya pawar wrote: If i give command as = g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8 this prints out all the protein water distance within 0.8nm. The data printed out is such that= t: 1466 5369 SOL 20624 OW 0.789894 (nm) t: 1467 5369 SOL 20624 OW 0.781596 (nm) t: 1469 5369 SOL 20624 OW 0.785377 (nm) t: 1473 5369 SOL 20624 OW 0.763485 (nm) t: 1474 5369 SOL 20624 OW 0.767805 (nm) t: 1475 5369 SOL 20624 OW 0.736003 (nm) t: 1476 5369 SOL 20624 OW 0.707953 (nm) t: 1477 5369 SOL 20624 OW 0.713135 (nm) t: 1478 5369 SOL 20624 OW 0.694042 (nm) t: 1480 5369 SOL 20624 OW 0.733907 (nm) t: 1481 5369 SOL 20624 OW 0.705245 (nm) t: 1482 5369 SOL 20624 OW 0.678473 (nm) t: 1483 5369 SOL 20624 OW 0.6288 (nm) t: 1492 5369 SOL 20624 OW 0.794252 (nm) t: 1496 5369 SOL 20624 OW 0.753049 (nm) t: 1497 5369 SOL 20624 OW 0.782796 (nm) t: 1498 5369 SOL 20624 OW 0.799607 (nm) t: 1499 5369 SOL 20624 OW 0.69987 (nm) t: 1500 5369 SOL 20624 OW 0.763511 (nm) t: 1501 5369 SOL 20624 OW 0.764072 (nm) t: 1502 5369 SOL 20624 OW 0.739181 (nm) t: 1503 5369 SOL 20624 OW 0.70336 (nm) In the above data can be seen that the time frame is not continuos. i.e. only the time at which the protein water distance within 0.8nm are shown. So is it possible to do g_analyze on this? None of the GROMACS tools are a replacement for thinking. What did you want to do with a list of interactions over time that were within 0.8nm? Run g_analyze is not an answer that will help you :) Mark On 01-Feb-2012, at 6:48 PM, Justin A. Lemkul wrote: aiswarya pawar wrote: Dear Gromacs Users, i have data for the distance between the protein and water atoms within a cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze on this data. The time frame in the output data is not continuous because of the cut off provided. So i would like to know how would the g_analyze would compute the data. I'm not clear on what you're trying to do. g_analyze performs simple statistical operations (averages, error estimates) on the input data. If there are discontinuities (which I do not understand the nature of), they come from the g_dist data, not what g_analyze is doing. Please provide a more clear description of what you are doing, including all relevant commands, and examples of the data files, 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 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 analysis tools for Namd output
On 2/02/2012 4:35 AM, PAUL NEWMAN wrote: Dear Gromacs users, I want to use the Gromacs analysis tools for analyzing Namd output files (*.dcd files) I just installed Gromacs 4.5.4 and it works well. In addition I installed VMD 1.9 and set up VMD_PLUGIN_PATH=/home/vmd-1.9/plugins/LINUXAMD64/molfile/ (Here it is located the dcdplugin.so ) I verified that VMD_PLUGIN_PATH is pointing out to the right folder. However when I run for example g_rmsf_d -f file.dcd -s file.pdb I got the following error The file format of file.dcd is not a known trajectory format to GROMACS. Please make sure that the file is a trajectory! GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins. This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD. No plugin for dcd found Am I doing something wrong? Do I need to do something else? Any help and advise will be highly appreciate it Maybe your GROMACS is 32bit and your VMD is 64bit. These would have to match. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] g_rdf
d(r) = (N/V)*g(r) Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mohammad agha Sent: Thursday, 2 February 2012 3:48 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_rdf Dear Prof. Thank you very much from your reply. Is your mean that density=(N/V)*g(r), where N is the number of total atoms in box not in the shell and V is the volume of box not in the shell? Best Regards Sara From: Dallas Warren dallas.war...@monash.edumailto:dallas.war...@monash.edu To: Discussion list for GROMACS users gmx-users@gromacs.orgmailto:gmx-users@gromacs.org Sent: Wednesday, February 1, 2012 2:12 AM Subject: RE: [gmx-users] g_rdf An RDF is normalised to the density for the entire box, so you should simply be using that. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edumailto:dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.orgmailto:gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mohammad agha Sent: Tuesday, 31 January 2012 7:26 PM To: gmx-users@gromacs.orgmailto:gmx-users@gromacs.org Subject: [gmx-users] g_rdf Dear Prof. I am confused about generation a radial density graph (density vs distance from center of mass), I know that I should use g_rdf. Then I count the number of atoms in the shells around the COM of special group by trjorder -com -nshell -r , next I use from this formula for compute the density: density = (dN/4*pi*dr*r^2)*g(r), where dN, dr, r and g(r) are the number of atoms in each shell, wide of shell, radius of COM of special group, and averaged RDF in each shell, respectively. While the plot of g(r) is consistent with published previous results but density has not consistence with them, I think that I am wrong in compute the density. Please help me. Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.orgmailto: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.orgmailto: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] Minimization Problems
Hello, I've recently been having trouble with my simulations blowing up. Specifically, This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size for a few interactions, with each of them approaching inf. Can anyone find anything glaringly wrong with my .mdp? Thanks, Alex Seling title = Minimization of alpha-synuclein cpp = /lib/cpp -traditional define = -DFLEXIBLE integrator = sd constraints = none tinit = 0 dt = 0.001 nsteps = 100 emtol = 0.1 emstep = 0.1 nstcgsteep = 1000 bd-fric = 0 nstlog = 50 nstenergy = 1 gen_temp = 273 gb_epsilon_solvent = 78.3 implicit_solvent = GBSA gb_algorithm = Still nstcomm = 10 xtc_precision = 1000 gen_vel = yes nstxtcout = 0 nstxout = 100 pbc = no energygrps = system nstfout = 0 nstvout = 0 niter = 20 nstlist = 10 -- 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] Minimization Problems
On Thu, Feb 2, 2012 at 12:36 PM, Alex Seling selin...@msu.edu wrote: Hello, I've recently been having trouble with my simulations blowing up. Specifically, This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size for a few interactions, with each of them approaching inf. Can anyone find anything glaringly wrong with my .mdp? Thanks, Alex Seling title = Minimization of alpha-synuclein cpp = /lib/cpp -traditional define = -DFLEXIBLE integrator = sd constraints = none tinit = 0 dt = 0.001 nsteps = 100 emtol = 0.1 emstep = 0.1 nstcgsteep = 1000 bd-fric = 0 nstlog = 50 nstenergy = 1 gen_temp = 273 gb_epsilon_solvent = 78.3 implicit_solvent = GBSA gb_algorithm = Still nstcomm = 10 xtc_precision = 1000 gen_vel = yes nstxtcout = 0 nstxout = 100 pbc = no energygrps = system nstfout = 0 nstvout = 0 niter = 20 nstlist = 10 it's more about your .gro file (system), less about the .mdp file. -- gmx-users mailing list gmx-userstheromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Minimization Problems
On 2/02/2012 3:36 PM, Alex Seling wrote: Hello, I've recently been having trouble with my simulations blowing up. Specifically, This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size for a few interactions, with each of them approaching inf. The usual advice and diagnostic procedure can be found here http://www.gromacs.org/Documentation/Terminology/Blowing_Up Can anyone find anything glaringly wrong with my .mdp? No constraints often requires a time step of 0.0005ps. Mark Thanks, Alex Seling title = Minimization of alpha-synuclein cpp = /lib/cpp -traditional define = -DFLEXIBLE integrator = sd constraints = none tinit = 0 dt = 0.001 nsteps = 100 emtol = 0.1 emstep = 0.1 nstcgsteep = 1000 bd-fric = 0 nstlog = 50 nstenergy = 1 gen_temp = 273 gb_epsilon_solvent = 78.3 implicit_solvent = GBSA gb_algorithm = Still nstcomm = 10 xtc_precision = 1000 gen_vel = yes nstxtcout = 0 nstxout = 100 pbc = no energygrps = system nstfout = 0 nstvout = 0 niter = 20 nstlist = 10 -- 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] Minimization Problems
On 2/02/2012 3:42 PM, lina wrote: On Thu, Feb 2, 2012 at 12:36 PM, Alex Selingselin...@msu.edu wrote: Hello, I've recently been having trouble with my simulations blowing up. Specifically, This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size for a few interactions, with each of them approaching inf. Can anyone find anything glaringly wrong with my .mdp? Thanks, Alex Seling title = Minimization of alpha-synuclein cpp = /lib/cpp -traditional define = -DFLEXIBLE integrator = sd constraints = none tinit = 0 dt = 0.001 nsteps = 100 emtol = 0.1 emstep = 0.1 nstcgsteep = 1000 bd-fric = 0 nstlog = 50 nstenergy = 1 gen_temp = 273 gb_epsilon_solvent = 78.3 implicit_solvent = GBSA gb_algorithm = Still nstcomm = 10 xtc_precision = 1000 gen_vel = yes nstxtcout = 0 nstxout = 100 pbc = no energygrps = system nstfout = 0 nstvout = 0 niter = 20 nstlist = 10 it's more about your .gro file (system), less about the .mdp file. Can be either. Integration from a silly starting point (.gro) can be unstable, as can integration of a silly Hamiltonian (partly due to .mdp). Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with make_ndx
Please suggest me the exact way to include dppc coordinates in topol.top file. On Wed, Feb 1, 2012 at 5:06 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 1/02/2012 6:25 PM, Anushree Tripathi wrote: But in coordinate file(.pdb file) ,I am not getting the atoms which belongs to DPPC. You cannot do anything unless you have a coordinate file that includes DPPC coordinates. I don't know how to express this any more clearly. only I have included the name of dppc.itp file like this: ;Include DPPC chain topology #include dppc.itp That's why I have found the atoms wich belongs to DPPC molecule from dppc.itp file itself. These numbers are not useful, as I have already explained. Mark On Wed, Feb 1, 2012 at 12:40 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 1/02/2012 6:04 PM, Anushree Tripathi wrote: When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is showing the following options: 0 System : 18379 atoms 1 Protein : 11739 atoms 2 Protein-H : 9135 atoms 3 C-alpha : 1173 atoms 4 Backbone: 3519 atoms 5 MainChain : 4693 atoms 6 MainChain+Cb: 5773 atoms 7 MainChain+H : 5842 atoms 8 SideChain : 5897 atoms 9 SideChain-H : 4442 atoms 10 Prot-Masses : 11739 atoms 11 non-Protein : 6640 atoms 12 Water : 6636 atoms 13 SOL : 6636 atoms 14 non-Water : 11743 atoms 15 Ion : 4 atoms 16 CL : 4 atoms 17 Water_and_ions : 6640 atoms So your system has 18K atoms, with 11K protein and the rest solvent and ions. As Justin suggested, this coordinate file does not have DPPC in it. for my work, I used 16|13 then 1|11.lastly I saved it using 'q'.But there is no option for DPPC (as given in tutorial we have to merge protein with DPPC).After runing the command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),it is showing error: Group DPPC not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. To troubleshoot the error,I have kept one more group in index.ndx file with number of atoms which I found from dppc.itp file(at the end of file) like this [DPPC] 123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 These numbers have to reference the atom numbers in the coordinate file, not the [moleculetype]. Since you've done the latter, you get the problem with T-coupling groups. But go back and use a coordinate file that actually has DPPC in it. Mark Again after running the grompp command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),I am getting the following error: Atom 1 in multiple T-Coupling groups (1 and 2). Please suggest me the reason as well as solution for this problem. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with make_ndx
Are you actually trying to simulate a membrane protein inside a DPPC bilayer though? If not, what is your reason for having it in your system? Also the topol.top file does not contain coordinates at all, only the forcefield parameterization. On 2012-02-02 12:11:44PM +0530, Anushree Tripathi wrote: Please suggest me the exact way to include dppc coordinates in topol.top file. On Wed, Feb 1, 2012 at 5:06 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 1/02/2012 6:25 PM, Anushree Tripathi wrote: But in coordinate file(.pdb file) ,I am not getting the atoms which belongs to DPPC. You cannot do anything unless you have a coordinate file that includes DPPC coordinates. I don't know how to express this any more clearly. only I have included the name of dppc.itp file like this: ;Include DPPC chain topology #include dppc.itp That's why I have found the atoms wich belongs to DPPC molecule from dppc.itp file itself. These numbers are not useful, as I have already explained. Mark On Wed, Feb 1, 2012 at 12:40 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 1/02/2012 6:04 PM, Anushree Tripathi wrote: When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is showing the following options: 0 System : 18379 atoms 1 Protein : 11739 atoms 2 Protein-H : 9135 atoms 3 C-alpha : 1173 atoms 4 Backbone: 3519 atoms 5 MainChain : 4693 atoms 6 MainChain+Cb: 5773 atoms 7 MainChain+H : 5842 atoms 8 SideChain : 5897 atoms 9 SideChain-H : 4442 atoms 10 Prot-Masses : 11739 atoms 11 non-Protein : 6640 atoms 12 Water : 6636 atoms 13 SOL : 6636 atoms 14 non-Water : 11743 atoms 15 Ion : 4 atoms 16 CL : 4 atoms 17 Water_and_ions : 6640 atoms So your system has 18K atoms, with 11K protein and the rest solvent and ions. As Justin suggested, this coordinate file does not have DPPC in it. for my work, I used 16|13 then 1|11.lastly I saved it using 'q'.But there is no option for DPPC (as given in tutorial we have to merge protein with DPPC).After runing the command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),it is showing error: Group DPPC not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. To troubleshoot the error,I have kept one more group in index.ndx file with number of atoms which I found from dppc.itp file(at the end of file) like this [DPPC] 123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 These numbers have to reference the atom numbers in the coordinate file, not the [moleculetype]. Since you've done the latter, you get the problem with T-coupling groups. But go back and use a coordinate file that actually has DPPC in it. Mark Again after running the grompp command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),I am getting the following error: Atom 1 in multiple T-Coupling groups (1 and 2). Please suggest me the reason as well as solution for this problem. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research
Re: [gmx-users] problem with make_ndx
On 2/02/2012 5:41 PM, Anushree Tripathi wrote: Please suggest me the exact way to include dppc coordinates in topol.top file. Start here http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations, as I think Justin already suggested. You should definitely learn (about) other people's workflows before attempting to adapt them to your needs. Mark On Wed, Feb 1, 2012 at 5:06 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 1/02/2012 6:25 PM, Anushree Tripathi wrote: But in coordinate file(.pdb file) ,I am not getting the atoms which belongs to DPPC. You cannot do anything unless you have a coordinate file that includes DPPC coordinates. I don't know how to express this any more clearly. only I have included the name of dppc.itp file like this: ;Include DPPC chain topology #include dppc.itp That's why I have found the atoms wich belongs to DPPC molecule from dppc.itp file itself. These numbers are not useful, as I have already explained. Mark On Wed, Feb 1, 2012 at 12:40 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 1/02/2012 6:04 PM, Anushree Tripathi wrote: When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is showing the following options: 0 System : 18379 atoms 1 Protein : 11739 atoms 2 Protein-H : 9135 atoms 3 C-alpha : 1173 atoms 4 Backbone: 3519 atoms 5 MainChain : 4693 atoms 6 MainChain+Cb: 5773 atoms 7 MainChain+H : 5842 atoms 8 SideChain : 5897 atoms 9 SideChain-H : 4442 atoms 10 Prot-Masses : 11739 atoms 11 non-Protein : 6640 atoms 12 Water : 6636 atoms 13 SOL : 6636 atoms 14 non-Water : 11743 atoms 15 Ion : 4 atoms 16 CL : 4 atoms 17 Water_and_ions : 6640 atoms So your system has 18K atoms, with 11K protein and the rest solvent and ions. As Justin suggested, this coordinate file does not have DPPC in it. for my work, I used 16|13 then 1|11.lastly I saved it using 'q'.But there is no option for DPPC (as given in tutorial we have to merge protein with DPPC).After runing the command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),it is showing error: Group DPPC not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. To troubleshoot the error,I have kept one more group in index.ndx file with number of atoms which I found from dppc.itp file(at the end of file) like this [DPPC] 123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 These numbers have to reference the atom numbers in the coordinate file, not the [moleculetype]. Since you've done the latter, you get the problem with T-coupling groups. But go back and use a coordinate file that actually has DPPC in it. Mark Again after running the grompp command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),I am getting the following error: Atom 1 in multiple T-Coupling groups (1 and 2). Please suggest me the reason as well as solution for this problem. -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with make_ndx
Yes I want to simulate the protein inside DPPC bilayer but how could I make the index file. Everytime it is showing error that no DPPC found in index file. On Thu, Feb 2, 2012 at 12:18 PM, Peter C. Lai p...@uab.edu wrote: Are you actually trying to simulate a membrane protein inside a DPPC bilayer though? If not, what is your reason for having it in your system? Also the topol.top file does not contain coordinates at all, only the forcefield parameterization. On 2012-02-02 12:11:44PM +0530, Anushree Tripathi wrote: Please suggest me the exact way to include dppc coordinates in topol.top file. On Wed, Feb 1, 2012 at 5:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 1/02/2012 6:25 PM, Anushree Tripathi wrote: But in coordinate file(.pdb file) ,I am not getting the atoms which belongs to DPPC. You cannot do anything unless you have a coordinate file that includes DPPC coordinates. I don't know how to express this any more clearly. only I have included the name of dppc.itp file like this: ;Include DPPC chain topology #include dppc.itp That's why I have found the atoms wich belongs to DPPC molecule from dppc.itp file itself. These numbers are not useful, as I have already explained. Mark On Wed, Feb 1, 2012 at 12:40 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 1/02/2012 6:04 PM, Anushree Tripathi wrote: When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is showing the following options: 0 System : 18379 atoms 1 Protein : 11739 atoms 2 Protein-H : 9135 atoms 3 C-alpha : 1173 atoms 4 Backbone: 3519 atoms 5 MainChain : 4693 atoms 6 MainChain+Cb: 5773 atoms 7 MainChain+H : 5842 atoms 8 SideChain : 5897 atoms 9 SideChain-H : 4442 atoms 10 Prot-Masses : 11739 atoms 11 non-Protein : 6640 atoms 12 Water : 6636 atoms 13 SOL : 6636 atoms 14 non-Water : 11743 atoms 15 Ion : 4 atoms 16 CL : 4 atoms 17 Water_and_ions : 6640 atoms So your system has 18K atoms, with 11K protein and the rest solvent and ions. As Justin suggested, this coordinate file does not have DPPC in it. for my work, I used 16|13 then 1|11.lastly I saved it using 'q'.But there is no option for DPPC (as given in tutorial we have to merge protein with DPPC).After runing the command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),it is showing error: Group DPPC not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. To troubleshoot the error,I have kept one more group in index.ndx file with number of atoms which I found from dppc.itp file(at the end of file) like this [DPPC] 123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 These numbers have to reference the atom numbers in the coordinate file, not the [moleculetype]. Since you've done the latter, you get the problem with T-coupling groups. But go back and use a coordinate file that actually has DPPC in it. Mark Again after running the grompp command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),I am getting the following error: Atom 1 in multiple T-Coupling groups (1 and 2). Please suggest me the reason as well as solution for this problem. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe
[gmx-users] how to make the SiO2 host to be neutral ?
Hi, I'm studying the diffusion system of some guest into zeolite structure (SiO2) assumed to be rigid body. My question is about making the host neutral. I obtained the unit cell of zeolite structure from the web. The structure exhibit net charge. (If I give some charge to Si and O which satisfies qSi+qO=0) In other words, the number of O is not the same as the twice of that of Si. I guess that some residue O is necessary to synthesis the system which is combined with a lot of identical unit cell. How can I solve it?? I think if I continue the study with net charged zeolite, there can exists some finite size effects. Can I delete the residue O atoms that does not connect with Si in the system that I made with a lot of unit cell. -- 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] problem with make_ndx
Ok. You will: 1. Need an actual DPPC bilayer. You can either make one from scratch (using something like VMD), or use pre-equilibrated patches from other people (like the ones from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies) (dppc128.pdb from that site). 2a. The bilayer and parameters by itself should be able to pass a simple grompp energy minimization mdp file without any errors (notifications are ok). Practice making a .top file with forcefield.itp, dppc.itp , lipid.itp, spc.itp and [ molecules ] section with the # of lipid molecules in the lipid-only .gro file. Then take a simple em.mdp and try to run grompp using your .top file and .gro file. 2b. Make sure your protein is properly parameterized. It too should be able to pass a grompp simple energy minimization preprocessing without any fatal errors by itself. 3. A way to insert your membrane protein into the bilayer/solvent complex. I think Justin uses InflateGRO method but some of us use g_membed. Orient the protein to the proper coordinates within the lipid/solvent system, and folllow the insertion protocol. At some point you will need to merge the Protein, DPPC, and water atom coordinates into a single .gro file and also merge all of the parameters (.itp) into a single top file. As Mark said, pay attention to all everything on this page: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html On 2012-02-02 12:36:54PM +0530, Anushree Tripathi wrote: Yes I want to simulate the protein inside DPPC bilayer but how could I make the index file. Everytime it is showing error that no DPPC found in index file. On Thu, Feb 2, 2012 at 12:18 PM, Peter C. Lai p...@uab.edu wrote: Are you actually trying to simulate a membrane protein inside a DPPC bilayer though? If not, what is your reason for having it in your system? Also the topol.top file does not contain coordinates at all, only the forcefield parameterization. On 2012-02-02 12:11:44PM +0530, Anushree Tripathi wrote: Please suggest me the exact way to include dppc coordinates in topol.top file. On Wed, Feb 1, 2012 at 5:06 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 1/02/2012 6:25 PM, Anushree Tripathi wrote: But in coordinate file(.pdb file) ,I am not getting the atoms which belongs to DPPC. You cannot do anything unless you have a coordinate file that includes DPPC coordinates. I don't know how to express this any more clearly. only I have included the name of dppc.itp file like this: ;Include DPPC chain topology #include dppc.itp That's why I have found the atoms wich belongs to DPPC molecule from dppc.itp file itself. These numbers are not useful, as I have already explained. Mark On Wed, Feb 1, 2012 at 12:40 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 1/02/2012 6:04 PM, Anushree Tripathi wrote: When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it is showing the following options: 0 System : 18379 atoms 1 Protein : 11739 atoms 2 Protein-H : 9135 atoms 3 C-alpha : 1173 atoms 4 Backbone: 3519 atoms 5 MainChain : 4693 atoms 6 MainChain+Cb: 5773 atoms 7 MainChain+H : 5842 atoms 8 SideChain : 5897 atoms 9 SideChain-H : 4442 atoms 10 Prot-Masses : 11739 atoms 11 non-Protein : 6640 atoms 12 Water : 6636 atoms 13 SOL : 6636 atoms 14 non-Water : 11743 atoms 15 Ion : 4 atoms 16 CL : 4 atoms 17 Water_and_ions : 6640 atoms So your system has 18K atoms, with 11K protein and the rest solvent and ions. As Justin suggested, this coordinate file does not have DPPC in it. for my work, I used 16|13 then 1|11.lastly I saved it using 'q'.But there is no option for DPPC (as given in tutorial we have to merge protein with DPPC).After runing the command (grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),it is showing error: Group DPPC not found in indexfile. Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp. In that case use the '-n' option. To troubleshoot the error,I have kept one more group in index.ndx file with number of atoms which I found from dppc.itp file(at the end of file) like this [DPPC] 123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 These
