[gmx-users] NMA Fatal Error
Hi Gmxers, I am doing a protein NMA with the mdp file like, === define = -DEFLEXIBLE constraints = none integrator = nm ; emtol = 0.1 emstep = 0.1 nsteps = 4000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 0 ; Frequency to update the neighbor list and long range forces ns_type = simple ; Method to determine neighbor list (simple, grid) ;vdwtype = switch vdwtype = cut-off rlist = 0.0 ; Cut-off for making neighbor list (short range forces) ;coulombtype = PME-switch ; Treatment of long range electrostatic interactions coulombtype = cut-off ;rcoulomb = 1.2 ; Short-range electrostatic cut-off rcoulomb = 0.0 ;rvdw = 1.2 ; Short-range Van der Waals cut-off rvdw = 0.0 pme_order = 4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 optimize_fft = yes pbc = no = However, it shows Fatal error: Constraints present with Normal Mode Analysis, this combination is not supported Since I put Constaints none, I really do not get it. Can someone help me? thanks, Yao -- 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] NMA proctocol
Hi Gmxers, For Normal Mode Analysis (NMA), even I did run several rounds to aim for machine precision, with smaller emtol stepwise, it still did not converge to 0.001 and the Fmax is about 0.5 or so. It is just lysozyme in 200 water molecules. I wonder if there is a systematic way to guarantee the convergence, or I have to await luck to come. Because I am pretty sure if I continue with NMA, I will get translational and rotational modes in final eigenfrequencies. thanks, Yao On 11/16/12 3:43 PM, Yao Yao wrote: Hi Gmxers, I am doing a protein NMA with the mdp file like, === define = -DEFLEXIBLE constraints = none integrator = nm ; emtol = 0.1 emstep = 0.1 nsteps = 4000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 0 ; Frequency to update the neighbor list and long range forces ns_type = simple ; Method to determine neighbor list (simple, grid) ;vdwtype = switch vdwtype = cut-off rlist = 0.0 ; Cut-off for making neighbor list (short range forces) ;coulombtype = PME-switch ; Treatment of long range electrostatic interactions coulombtype = cut-off ;rcoulomb = 1.2 ; Short-range electrostatic cut-off rcoulomb = 0.0 ;rvdw = 1.2 ; Short-range Van der Waals cut-off rvdw = 0.0 pme_order = 4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 optimize_fft = yes pbc = no = However, it shows Fatal error: Constraints present with Normal Mode Analysis, this combination is not supported Since I put Constaints none, I really do not get it. Can someone help me? The problem is a typo. You've set -DEFLEXIBLE instead of -DFLEXIBLE so rather than having flexible water as intended, you've got rigid water via the SETTLE algorithm, and constraints are still present. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/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] Hessian Unit
hi Gmxers, is the Hessian matrix unit in gmx is ps^(-2), or J *mol^(-1) nm^(-2)? thanks, Yao -- -- 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] Gmx Hessian
hi Gmxers, is the Hessian matrix unit in gmx is ps^(-2), or J *mol^(-1) nm^(-2)? thanks, Yao -- 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
Fw: [gmx-users] hessian conversion
Hi Gmxers, has anyone ever converted the GROMACS hessian (in ps^(-2)) to CHARMM hessian (in KCal/mol), even considering the individual unit, GROMACS hessian numbers are far bigger than those in CHARMM? thanks, Yao -- -- 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] hessian conversion
Hi Gmxers, has anyone ever converted the GROMACS hessian (in ps^(-2)) to CHARMM hessian (in KCal/mol), even considering the individual unit, GROMACS hessian numbers are far bigger than those in CHARMM? thanks, Yao -- 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] Water Shell Density
Hi Gmxers, Is there a way to calculate the density of water in a protein hydration layer, like from 5 A to 10 A (radius) from the protein surface? Thanks, Yao -- 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] water channel
Hi Gmxers, Happy Valentine's Day! Sorry, I am still simulating a protein that has water channel. I was just wondering if there is a way to calculate the water density in the channel throughout my trajectory. I was lucky enough to run a NPT simulation. So I guess I can use g_energy to directly get density. But since the number of the channel water is quite dynamic, I do not think I can separate energy group for them in my mdp. Could someone help me with this? Thanks, Yao -- 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] Water Shell Density
Hi Gmxers, Is there a way to calculate the density of water in a protein hydration layer, like from 5 A to 10 A (radius) from the protein surface? Thanks, Yao-- 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] co-solvent simulation
I am simulating a protein in glycerol solution in amber03 ff and followed http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents;. Since glycerol is not available in amber03.ff by default, I built it in the ffbonded.itp and aminoacids.rtp. For test purpose, I then made a itp for it and solvate it as a protein and changed .top file accordingly, everything seems fine when I grompp, but when I insert it as a co-solvent, it shows like that I never did claim any bond angles, dihedrals, even when I #include its .itp and change #mols in my new topology. I guess the problem is if I do not claim the co-solvent as a protein, ff will not go to ffbonded.itp to recognize the new interactions. Is there any other file for co-solvent interactions I need to change? Thanks, Yao-- 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] co-solvent simulation
Hi Mark, Thanks for your reply. I have not figured out what the problem. BUt I am thinking if I have two proteins in my system, like simulating the protein-protein interaction, what I should call the second protein for [moleculetype] in my .top, still protein? Thanks, Yao From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, February 11, 2012 9:39 PM Subject: Re: [gmx-users] co-solvent simulation On 12/02/2012 4:16 PM, Yao Yao wrote: I am simulating a protein in glycerol solution in amber03 ff and followed http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents;. Since glycerol is not available in amber03.ff by default, I built it in the ffbonded.itp You should not need to touch this file to model glycerol. There are no atom or interaction types that are materially different from those on peptide side chains. and aminoacids.rtp. For test purpose, I then made a itp for it and solvate it as a protein and changed .top file accordingly, everything seems fine when I grompp, but when I insert it as a co-solvent, it shows like that I never did claim any bond angles, dihedrals, even when I #include its .itp and change #mols in my new topology. You need to work out what is different in the two cases. The diff tool can be useful here. There is no fundamental difference in the .top construction for the two cases you are considering - only in construction of the initial coordinates. I guess the problem is if I do not claim the co-solvent as a protein, ff will not go to ffbonded.itp to recognize the new interactions. Is there any other file for co-solvent interactions I need to change? The ffbonded.itp file is #included regardless of what you name your moleculetypes. You may not be #including the correct one - but then again I think you should only have the standard one in the first place. Mark -- 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] co-solvent simulation
Actually even I follow the http://www.gromacs.org/Documentation/How-tos/Mixed_Solventsand try the built-in ureaas co-solvent, it has the same problem (solvate urea as protein can work, but does not work if you consider it as co-solvent). I do not know if anyone has met the same problem before. Thanks, Yao - Forwarded Message - From: Yao Yao ya...@ymail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, February 11, 2012 10:47 PM Subject: Re: [gmx-users] co-solvent simulation Hi Mark, Thanks for your reply. I have not figured out what the problem. BUt I am thinking if I have two proteins in my system, like simulating the protein-protein interaction, what I should call the second protein for [moleculetype] in my .top, still protein? Thanks, Yao From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, February 11, 2012 9:39 PM Subject: Re: [gmx-users] co-solvent simulation On 12/02/2012 4:16 PM, Yao Yao wrote: I am simulating a protein in glycerol solution in amber03 ff and followed http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents;. Since glycerol is not available in amber03.ff by default, I built it in the ffbonded.itp You should not need to touch this file to model glycerol. There are no atom or interaction types that are materially different from those on peptide side chains. and aminoacids.rtp. For test purpose, I then made a itp for it and solvate it as a protein and changed .top file accordingly, everything seems fine when I grompp, but when I insert it as a co-solvent, it shows like that I never did claim any bond angles, dihedrals, even when I #include its .itp and change #mols in my new topology. You need to work out what is different in the two cases. The diff tool can be useful here. There is no fundamental difference in the .top construction for the two cases you are considering - only in construction of the initial coordinates. I guess the problem is if I do not claim the co-solvent as a protein, ff will not go to ffbonded.itp to recognize the new interactions. Is there any other file for co-solvent interactions I need to change? The ffbonded.itp file is #included regardless of what you name your moleculetypes. You may not be #including the correct one - but then again I think you should only have the standard one in the first place. Mark -- 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] co-solvent simulation
Please disregard my previous email. I made a minor mistake when I built the .top file. Thanks, Yao From: Yao Yao ya...@ymail.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Saturday, February 11, 2012 11:06 PM Subject: [gmx-users] co-solvent simulation Actually even I follow the http://www.gromacs.org/Documentation/How-tos/Mixed_Solventsand try the built-in ureaas co-solvent, it has the same problem (solvate urea as protein can work, but does not work if you consider it as co-solvent). I do not know if anyone has met the same problem before. Thanks, Yao - Forwarded Message - From: Yao Yao ya...@ymail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, February 11, 2012 10:47 PM Subject: Re: [gmx-users] co-solvent simulation Hi Mark, Thanks for your reply. I have not figured out what the problem. BUt I am thinking if I have two proteins in my system, like simulating the protein-protein interaction, what I should call the second protein for [moleculetype] in my .top, still protein? Thanks, Yao From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, February 11, 2012 9:39 PM Subject: Re: [gmx-users] co-solvent simulation On 12/02/2012 4:16 PM, Yao Yao wrote: I am simulating a protein in glycerol solution in amber03 ff and followed http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents;. Since glycerol is not available in amber03.ff by default, I built it in the ffbonded.itp You should not need to touch this file to model glycerol. There are no atom or interaction types that are materially different from those on peptide side chains. and aminoacids.rtp. For test purpose, I then made a itp for it and solvate it as a protein and changed .top file accordingly, everything seems fine when I grompp, but when I insert it as a co-solvent, it shows like that I never did claim any bond angles, dihedrals, even when I #include its .itp and change #mols in my new topology. You need to work out what is different in the two cases. The diff tool can be useful here. There is no fundamental difference in the .top construction for the two cases you are considering - only in construction of the initial coordinates. I guess the problem is if I do not claim the co-solvent as a protein, ff will not go to ffbonded.itp to recognize the new interactions. Is there any other file for co-solvent interactions I need to change? The ffbonded.itp file is #included regardless of what you name your moleculetypes. You may not be #including the correct one - but then again I think you should only have the standard one in the first place. Mark -- 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 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] protein in solution
Hi Gmxers, I plan to simulate a protein in an 1M glycerol solution. How can I control the concentration and insert the protein into my solution. Thanks, Yao -- 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_select dynamic indices
Hi Gmxers, I used g_dist to find all water molecules within 5 Angstrom of a protein in a trajectory with a little surprise that gromacs directly prints out those water on my screen rather than in an output file. Since in each frame, those water molecules are not the same, I realize I need to make a dynamic index or indices for them. However I do not see any flag I could possibly introduce those water in g_select and then use -on flag to produce a dynamic index. Anyone has met this before? Thanks, Yao-- 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_select dynamic indices
Hi Justin, Thanks for your hints. I feel the string in g_select is pretty much like tck/tl in VMD. However I have not figured out the way to select a customized group defined in .ndx file. And one more question I have, maybe more general, if I have, say, 100 frames, g_select will give me 100 dynamic indices in the .ndx file, I am wondering if there is a way (might be some script) that can help me choose automatically for further processing, like g_hbond, and then I can program to collect all frames and average them. In other words, there many commands in gromacs that require users to Select a group, I am wondering if I can make this choice in a script rather than when I see the prompt. thanks, Yao From: Justin A. Lemkul jalem...@vt.edu To: Yao Yao ya...@ymail.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 30, 2011 1:57 PM Subject: Re: [gmx-users] g_select dynamic indices Yao Yao wrote: Hi Gmxers, I used g_dist to find all water molecules within 5 Angstrom of a protein in a trajectory with a little surprise that gromacs directly prints out those water on my screen rather than in an output file. According to g_dist -h, that's what you should expect :) Since in each frame, those water molecules are not the same, I realize I need to make a dynamic index or indices for them. However I do not see any flag I could possibly introduce those water in g_select and then use -on flag to produce a dynamic index. The index groups are output by g_select. Try g_select -select help all for examples of how to create groups. -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] protein hydration shell water
Hi Gmxers, Anyone knows any command or flag that can extract the water within some distance from the surface of a protein? thanks, Yao Yao -- 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_hbond -hbn
Hi Gmxers, I used g_hbond -n protein.ndx -hbn output.xvg to get the index of all the atoms forming H-bond with the protein, but since H-Bonds should be dynamic as time evolves, I should see changing number of HBonds in the output.xvg which I have not seen yet. Kinda confused. Thanks, Yao -- 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] solvents in gmx
Hi Gmxers, Is there a way I can check all the kinds of solvents in gromacs? Apart from water, ethanol, ..., are there any Glycerol, Treholose, Thanks, Yao -- 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_hbond frames
Hi Gmxers, I ran g_hbond between my protein and water for a 3ns trajectory with 2 fs integration step but found the error, Cannot calculate autocorrelation of life times with less than two frames, I am quite sure my system is just a regular protein in a cubic water box. And the size of trajectory is big with no error messages when finished. So it should not be just a couple of frames. Anyone met this before? Thanks, Yao -- 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] where are Density and Volume?
Hi, I wanna get Density and Volume of my system after simulation. I found in tutorials by Justin and kerrigan?, that g_energy -f *.edr -o should work, but I do not find in my version 4.5.1 and 4.5.4. That is kind of weird. Thanks, Yao-- 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] where are Density and Volume?
Hi Justin, thanks, that is just initial value, no fluctuation over time. yao From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, October 13, 2011 10:24 AM Subject: Re: [gmx-users] where are Density and Volume? Yao Yao wrote: Hi Justin, It is NVE. Is there a consistent way I can know my D and V? Then you've got the same case as NVT (for these values, anyway) - volume and density are fixed at whatever value they started at. editconf should have printed this somewhere along the way. -Justin Thanks, Yao *From:* Justin A. Lemkul jalem...@vt.edu *To:* Yao Yao ya...@ymail.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, October 13, 2011 9:58 AM *Subject:* Re: [gmx-users] where are Density and Volume? Yao Yao wrote: Hi, I wanna get Density and Volume of my system after simulation. I found in tutorials by Justin and kerrigan?, that g_energy -f *.edr -o should work, but I do not find in my version 4.5.1 and 4.5.4. That is kind of weird. Was it an NVT simulation? If so, those terms are not written because they are, by definition, constant. -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 -- 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 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 Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/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 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] where are Density and Volume?
Hi, Justin Ok, I see the problem. Like your tutorial, I used cpt for NVT/NPT to mdrun/continue NVE production run. So though I did not set V or P constraint in NVE mdp, it still keeps them as constant, like my NVE did not work. Am I supposed to do so if I wanna simulate NVE? Thanks, Yao From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, October 13, 2011 10:42 AM Subject: Re: [gmx-users] where are Density and Volume? Yao Yao wrote: Hi Justin, thanks, that is just initial value, no fluctuation over time. Right. The volume is constant, therefore the initial values of density and volume are always the same. -Justin yao *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, October 13, 2011 10:24 AM *Subject:* Re: [gmx-users] where are Density and Volume? Yao Yao wrote: Hi Justin, It is NVE. Is there a consistent way I can know my D and V? Then you've got the same case as NVT (for these values, anyway) - volume and density are fixed at whatever value they started at. editconf should have printed this somewhere along the way. -Justin Thanks, Yao *From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *To:* Yao Yao ya...@ymail.com mailto:ya...@ymail.com; Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Thursday, October 13, 2011 9:58 AM *Subject:* Re: [gmx-users] where are Density and Volume? Yao Yao wrote: Hi, I wanna get Density and Volume of my system after simulation. I found in tutorials by Justin and kerrigan?, that g_energy -f *.edr -o should work, but I do not find in my version 4.5.1 and 4.5.4. That is kind of weird. Was it an NVT simulation? If so, those terms are not written because they are, by definition, constant. -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 -- 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 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 Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/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 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 -- 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 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 Blacksburg, VA
Re: [gmx-users] where are Density and Volume?
Hi Justin, Just curious. what is inside .cpt file,is there a way I can change it in readable format? I also notice that every mdrun step I got a state.cpt and state_prev.cpt as well, any difference between the two? And using .cpt seems a little faster (a couple of hours or so) than without using it for the same time length simulation, do you happen to know the reason? Thanks, yao From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, October 13, 2011 11:28 AM Subject: Re: [gmx-users] where are Density and Volume? Yao Yao wrote: Hi, Justin Ok, I see the problem. Like your tutorial, I used cpt for NVT/NPT to mdrun/continue NVE production run. So though I did not set V or P constraint in NVE mdp, it still keeps them as constant, like my NVE did not work. Am I supposed to do so if I wanna simulate NVE? NVE will keep the energy constant under the set conditions. I do not know why P is constant; with V being constant (by definition), P should fluctuate under NVE. Providing a .cpt file from a previous NVT or NPT will define the conditions under which NVE is run (i.e. what energy is to be maintained). -Justin Thanks, Yao *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Thursday, October 13, 2011 10:42 AM *Subject:* Re: [gmx-users] where are Density and Volume? Yao Yao wrote: Hi Justin, thanks, that is just initial value, no fluctuation over time. Right. The volume is constant, therefore the initial values of density and volume are always the same. -Justin yao *From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Thursday, October 13, 2011 10:24 AM *Subject:* Re: [gmx-users] where are Density and Volume? Yao Yao wrote: Hi Justin, It is NVE. Is there a consistent way I can know my D and V? Then you've got the same case as NVT (for these values, anyway) - volume and density are fixed at whatever value they started at. editconf should have printed this somewhere along the way. -Justin Thanks, Yao *From:* Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu *To:* Yao Yao ya...@ymail.com mailto:ya...@ymail.com mailto:ya...@ymail.com mailto:ya...@ymail.com; Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Sent:* Thursday, October 13, 2011 9:58 AM *Subject:* Re: [gmx-users] where are Density and Volume? Yao Yao wrote: Hi, I wanna get Density and Volume of my system after simulation. I found in tutorials by Justin and kerrigan?, that g_energy -f *.edr -o should work, but I do not find in my version 4.5.1 and 4.5.4. That is kind of weird. Was it an NVT simulation? If so, those terms are not written because they are, by definition, constant. -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 -- 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 list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto: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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
[gmx-users] QM/MM/MD Semi-empirical Error
Hi Guys, I met a problem when I ran QM/MM/MD using semi-empirical method in gmx407+mopac7, - Subscript out of range on file line 659, procedure moldat. Attempt to access the 0-th element of variable eheat. Aborted -- I googled it, but there seems no archived info online. Has anyone met this before? Thanks, Yao Yao -- 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 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] QM/MM/MD Semi-empirical Error
Hi Guys, I met a problem when I ran QM/MM/MD using semi-empirical method in gmx407+mopac7, Subscript out of range on file line 1002, procedure domldt. Attempt to access the 161-th element of variable labels. Aborted - Has anyone met this before? Thanks, yao - Forwarded Message - From: Yao Yao ya...@ymail.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Tuesday, September 13, 2011 12:14 AM Subject: [gmx-users] QM/MM/MD Semi-empirical Error Hi Guys, I met a problem when I ran QM/MM/MD using semi-empirical method in gmx407+mopac7, - Subscript out of range on file line 659, procedure moldat. Attempt to access the 0-th element of variable eheat. Aborted -- I googled it, but there seems no archived info online. Has anyone met this before? Thanks, Yao Yao -- 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 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 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 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] gbsa.itp problem
Hi All, when I grompp for energy minimization, I met the error like, -- Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs407/share/gromacs/top/ffamber03.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffnonbonded.itp WARNING 1 [file ffnonbonded.itp, line 38]: Overriding atomtype NA Opening library file /share/apps/gromacs407/share/gromacs/top/ffbonded.itp Opening library file /share/apps/gromacs407/share/gromacs/top/gbsa.itp ERROR 1 [file gbsa.itp, line 1]: Invalid directive implicit_genborn_params --- Program grompp, VERSION 4.0.7 Source code file: toppush.c, line: 756 Fatal error: Unknown bond_atomtype 0.172 --- Since in the version 4.0.7 there is no gbsa.itp, I simply copied the file with the same name from gmx 4.5-4 and introduced ffamber03 force field into 4.0.7. I understand updating to 4.5.X will solve this problem, but for testing my QMMM semi-empirical implementation, I have to use gmx version 4.0.7, at least for now. So I am wondering if there is any way I can solve it in 4.0.7. Thanks, Yao-- 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] gbsa.itp problem
I mean if I still want to use the introduced amber03 ff, when I solvate it as normal, it asks for gbsa.itp, -- Fatal error: Library file gbsa.itp not found in current dir nor in default directories. (You can set the directories to search with the GMXLIB path variable) -- So is there any other file I need to change? thanks, yao From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, September 6, 2011 3:21 PM Subject: Re: [gmx-users] gbsa.itp problem Yao Yao wrote: Hi Justin, Thanks for your reply. Is there a way I can use explicit water to get rid of the error? Solvate as you would any normal system and don't try to use force field files from newer versions. -Justin Thanks, Yao *From:* Justin A. Lemkul jalem...@vt.edu *To:* Yao Yao ya...@ymail.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Tuesday, September 6, 2011 2:42 PM *Subject:* Re: [gmx-users] gbsa.itp problem Yao Yao wrote: Hi All, when I grompp for energy minimization, I met the error like, -- Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs407/share/gromacs/top/ffamber03.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffnonbonded.itp WARNING 1 [file ffnonbonded.itp, line 38]: Overriding atomtype NA Opening library file /share/apps/gromacs407/share/gromacs/top/ffbonded.itp Opening library file /share/apps/gromacs407/share/gromacs/top/gbsa.itp ERROR 1 [file gbsa.itp, line 1]: Invalid directive implicit_genborn_params --- Program grompp, VERSION 4.0.7 Source code file: toppush.c, line: 756 Fatal error: Unknown bond_atomtype 0.172 --- Since in the version 4.0.7 there is no gbsa.itp, I simply copied the file with the same name from gmx 4.5-4 and introduced ffamber03 force field into 4.0.7. I understand updating to 4.5.X will solve this problem, but for testing my QMMM semi-empirical implementation, I have to use gmx version 4.0.7, at least for now. So I am wondering if there is any way I can solve it in 4.0.7. You can't do implicit solvent simulations with a version 4.5. -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 -- 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 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] pdb2gmx response time
Hi All, when I pdb2gmx on a very small (~20 atoms) peptide, it seemingly got stuck in the middle, showing Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.rtp Opening library file /share/apps/gromacs407/share/gromacs/top/aminoacids.dat Opening library file /share/apps/gromacs407/share/gromacs/top/aminoacids.dat WARNING: masses will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /share/apps/gromacs407/share/gromacs/top/atommass.dat Entries in atommass.dat: 178 WARNING: vdwradii will be determined based on residue and atom names, this can deviate from the real mass of the atom type Opening library file /share/apps/gromacs407/share/gromacs/top/vdwradii.dat Entries in vdwradii.dat: 28 Opening library file /share/apps/gromacs407/share/gromacs/top/dgsolv.dat Entries in dgsolv.dat: 7 Opening library file /share/apps/gromacs407/share/gromacs/top/electroneg.dat Entries in electroneg.dat: 71 Opening library file /share/apps/gromacs407/share/gromacs/top/elements.dat Entries in elements.dat: 218 Opening library file /share/apps/gromacs407/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 1 residues with 14 atoms chain #res #atoms 1 '-' 1 14 No occupancies in AA.gro Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.atp Atomtype 1 Has anyone come across this before? Thanks, Yao -- 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] OPLS-AA Unknown Atomtype
Hi Justin, Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp, but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp Generated 338253 of the 338253 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 338253 of the 338253 1-4 parameter combinations ERROR 1 [file cro.top, line 37]: No default Bond types ERROR 2 [file cro.top, line 71]: No default Angle types ERROR 3 [file cro.top, line 72]: No default Angle types ERROR 4 [file cro.top, line 85]: No default Angle types ERROR 5 [file cro.top, line 91]: No default Ryckaert-Bell. types ERROR 6 [file cro.top, line 92]: No default Ryckaert-Bell. types ERROR 7 [file cro.top, line 93]: No default Ryckaert-Bell. types ERROR 8 [file cro.top, line 108]: No default Ryckaert-Bell. types ERROR 9 [file cro.top, line 112]: No default Proper Dih. types ERROR 10 [file cro.top, line 113]: No default Proper Dih. types ERROR 11 [file cro.top, line 114]: No default Proper Dih. types Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file cro.top, line 142]: System has non-zero total charge: -1.022478e+00 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 11 errors in input file(s) --- I do double-check those bondtypes, angles, and interactions mentioned in the errors, and I am pretty sure I have already declared those values in the ffoplsaabon.itp. Is there any other file I also need to mention those values? Thanks, Yao From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, August 23, 2011 2:07 PM Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype Yao Yao wrote: Hi Justin, Thanks for your reply. Here is the exact error message, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp --- Program grompp, VERSION 4.0.7 Source code file: toppush.c, line: 620 Fatal error: Unknown bond_atomtype CA1 --- ~~ I understand that I have not inserted CA1 into atomtypes.atp. because if I add CA1 as a new atom, I have to mention all bonds, angles, dihedrals of it. The atomtypes.atp file is irrelevant here; it is only used by pdb2gmx. What you are trying to avoid is what you have to do - if you introduce a new atom type and intend to use it in any bonded interactions, you must introduce relevant parameters for all the interactions in which it will participate. So I denoted the type of it as a known carbon atom in my topology file (in the attachment). I thought in OPLS-AA, CA1 can cite this known atom since CA1 is just a name. Names and types are different. You can name an atom anything you like, but atom types must be judiciously assigned. Meanwhile, in the ffbonded.itp and ffnonbonded.itp, I still use CA1 to give bonds, angles, and dihedrals of CA1. If you have inserted all of the correct parameters in these files, you would not receive the error above. Perhaps herein lies the problem - if you have modified ffnonbonded.itp (which belongs to the force field organization of the 4.5.x series), it will have no effect on a 4.0.7 executable, which is being called above. So (at least) one of two possibilities is true: 1. You're not using the Gromacs version you intend to. 2. You haven't introduced all of the parameters you need to. The bond_atomtype values are assigned in ffnonbonded.itp (counterintuitive, I know, but that's how
Re: [gmx-users] OPLS-AA Unknown Atomtype
HI Justin, I met these errors when I grompp to do 1st-time energy minimization before I planned to add the ions. So I do not think ions addition will help. And I double-checked the angles, bonds, mentioned in the ffoplsaabon.itp, they are there. So I do not know any other files I may need to modify. Thanks, yao From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, August 29, 2011 3:41 AM Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype Yao Yao wrote: Hi Justin, Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp, but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# checking input for internal consistency... processing topology... Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp Generated 338253 of the 338253 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 338253 of the 338253 1-4 parameter combinations ERROR 1 [file cro.top, line 37]: No default Bond types ERROR 2 [file cro.top, line 71]: No default Angle types ERROR 3 [file cro.top, line 72]: No default Angle types ERROR 4 [file cro.top, line 85]: No default Angle types ERROR 5 [file cro.top, line 91]: No default Ryckaert-Bell. types ERROR 6 [file cro.top, line 92]: No default Ryckaert-Bell. types ERROR 7 [file cro.top, line 93]: No default Ryckaert-Bell. types ERROR 8 [file cro.top, line 108]: No default Ryckaert-Bell. types ERROR 9 [file cro.top, line 112]: No default Proper Dih. types ERROR 10 [file cro.top, line 113]: No default Proper Dih. types ERROR 11 [file cro.top, line 114]: No default Proper Dih. types Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file cro.top, line 142]: System has non-zero total charge: -1.022478e+00 This total charge suggests that your topology is badly broken. processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note --- Program grompp, VERSION 4.0.7 Source code file: grompp.c, line: 986 Fatal error: There were 11 errors in input file(s) --- I do double-check those bondtypes, angles, and interactions mentioned in the errors, and I am pretty sure I have already declared those values in the ffoplsaabon.itp. Is there any other file I also need to mention those values? If these types were actually present in ffoplsaabon.itp, then you wouldn't get these errors. Double check again. -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 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] OPLS-AA Unknown Atomtype
Hi all, I am constructing a new molecule in OPLS force field. Though I modified ffbonded.itp, ffnonbonded.itp, atomtypes.atp aminoacids.rtp, it still gives error Unknown Molecule_Atomtype. I have opened all the files in the OPLS force field but really do not see any other files I could modify. Does anyone have this kind of problem before? Thanks, Yao -- 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_hbond simple question
Hi Guys, I am using g_hbond to analyze hbond between two groups. The manual says All hydrogen bonds between the two groups are analyzed. Does that mean even those hbonds do not hbond to neither of the two groups are still under consideration? Thanks, Yao -- 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] QMMM Semi-empirical Error
Hi Guys, I met a problem when I ran qmmm using semi-empirical method in gmx, Subscript out of range on file line 659, procedure moldat. Attempt to access the 0-th element of variable eheat. Aborted I googled it, but there seems no archived info online. Has anyone met this before? Thanks, Yao Yao-- 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] Fw: QMMM Semi-empirical Error
Hi Guys, I met a problem when I ran qmmm using semi-empirical method in gmx, Subscript out of range on file line 659, procedure moldat. Attempt to access the 0-th element of variable eheat. Aborted I googled it, but there seems no archived info online. Has anyone met this before? Thanks, Yao Yao-- 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] Mopac/Gmx QMMM
I am trying to compile mopac with gmx for qmmm calculation purpose and found the link http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMMis really helpful. However I can only download the on of the two required fortran files, gmxmop.f,but not the other, dcart.f. And since I am using linux, I would like to download libmopac.a,which is not available on the webpage. Could anyone share these files with me? I really appreciate it. Best, Yao -- 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] QMMM+NMA
Hi Gmxers, I am wondering if NMA has been introduced into QMMM part of gromacs. I am trying to get vibrational frequencies of proteins by normal mode analysis (NMA) in the framework of QMMM. Thanks, Yao -- 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] qmmm temp definition
Hi gmxers, I am working on qmmm treatment of a heat shock protein. Heat-sensitive part is treated quantum mechanically, while the other parts classically. I am hence wondering if it is available and applicable in gromacs that this qm part can be heated and cooled for temperature variation purpose, maybe like using the same index for qm part and defining it as a different temperature/energy group. Thanks, Yao -- 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] qmmm linking atom
Hi gmxers, I am just wondering how to give a linking atom's coordinates in a qmmm calculation generally.Would it be normal to take an arithmetic average of two neighboring qmmm-layer-bonding atoms' coordinates? Thanks, Yao -- 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] Eigenvectors
Hi Gmxers, I am just wondering if the eigenvectors in gromacs are normalized or not, and how to check that after the normal mode analysis/ thanks, Yao -- 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] Eigenvectors
Hi Gmxers, I am just wondering if the eigenvectors in gromacs are normalized or not, and how to check that after the normal mode analysis/ thanks, Yao -- 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] Eigenvectors
Hi Gmxers, I am just wondering if the eigenvectors in gromacs are normalized or not. thanks, Yao -- 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] Targeted Energy Minimization
Hi Gmxers, Is that possible that in mdp file, only a specifically-targeted part inside/of the protein is energy minimized (EM)? Like, just wanna EM the ligand or one out of the two proteins in protein-docking. Thanks in advance, Yao -- 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] charmm tip5p in Gmx 4.5.X
Hi Berk, Thanks for your reply. Actually I followed the fws-peptide simulation in Dr. JE Kerrigan's tutorial, but in charmm27 force field with tip5p water. Before several warnings in the simulation step, I found that even in energy minimization step the protein cannot be settled. I sent my mdp file to the forum, and got an ok from Justin. So I am concerned about the compatibility between tip5p and charmm force field in gromacs, as well as the potential improvement in the new version. Sincerely, Yao --- On Wed, 10/6/10, Berk Hess g...@hotmail.com wrote: From: Berk Hess g...@hotmail.com Subject: RE: [gmx-users] charmm tip5p in Gmx 4.5.2 To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, October 6, 2010, 10:02 AM Date: Wed, 6 Oct 2010 11:53:56 +0200 Subject: Re: [gmx-users] charmm tip5p in Gmx 4.5.2 From: szilard.p...@cbr.su.se To: gmx-users@gromacs.org Hi, Does anyone have an idea about what time the Gmx 4.5.2 will be released? Soon, if everything goes well in a matter of days. And in 4.5.2, would the modified tip5p.itp in charmm27 force field be the same as that in current git version? What is your motivation behind this question? Do you think there is something wrong wit the current tip5p.itp? Berk The git branch release-4-5-patches is the branch you want to look at. Whatever is in there will be in the release (unless it get removed :). -- Szilárd -- 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 -Inline Attachment Follows- -- 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] charmm tip5p in Gmx 4.5.2
Dear Gmxers, Does anyone have an idea about what time the Gmx 4.5.2 will be released?And in 4.5.2, would the modified tip5p.itp in charmm27 force field be the same as that in current git version? Thanks, Yao -- 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] charmm tip5p in Gmx 4.5.2
---BeginMessage--- Dear Gmxers, Does anyone have an idea about what time the Gmx 4.5.2 will be released?And in 4.5.2, would the modified tip5p.itp in charmm27 force field be the same as that in current git version? Thanks, Yao ---End Message--- -- 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_hbond segmentation fault
Hi Gmxers, Sorry, Eric and David, I cannot transfer my trr file to report a bug because of its huge size. It is just a regular protein with 70 Angstrom cubic TIP5P water box in Charmm27 force field. That's all of the system. But anyway, i included the mdp file in the attachment. Hopefully someone can help me. Many thanks, Yao --- On Wed, 9/29/10, Erik Marklund er...@xray.bmc.uu.se wrote: From: Erik Marklund er...@xray.bmc.uu.se Subject: Re: [gmx-users] g_hbond segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, September 29, 2010, 7:55 AM Hi, Could you file a bugzilla and attach the trr and tpr files please? If you do I'll try to sort it out today or at least this week. Erik Yao Yao skrev 2010-09-29 08.22: I tried without -dt or -e, still the same problem exists in either case. Thanks, Yao --- On Wed, 9/29/10, David van der Spoel sp...@xray.bmc.uu.se wrote: From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] g_hbond segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, September 29, 2010, 6:11 AM On 2010-09-29 08.02, Yao Yao wrote: Hi Gmxers, I used the command line, g_hbond -f tst.trr -s tst.tpr -ac test -e 500 -dt 1 and I got the message like, try without the -dt 1 -- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 2/10915 *Segmentation fault* __ Anyone knows what could be the reason for this Segmentation Fault ? A couple of Q's I am also curious, why do we need to swap Acceptors and Acceptors when merging hbonds? Does gromacs suggest that the number of different hydrogen bonds in trajectory should be the same as that of different atom-pairs within hydrogen bonding distance? Thanks, Yao -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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 -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 er...@xray.bmc.uu.se http://folding.bmc.uu.se/ -Inline Attachment Follows- -- gmx-users
[gmx-users] g_hbond segmentation fault
Hi Gmxers, I used the command line, g_hbond -f tst.trr -s tst.tpr -ac test -e 500 -dt 1 and I got the message like, -- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 2/10915 Segmentation fault __ Anyone knows what could be the reason for this Segmentation Fault ? A couple of Q's I am also curious, why do we need to swap Acceptors and Acceptors when merging hbonds? Does gromacs suggest that the number of different hydrogen bonds in trajectoryshould be the same as that of different atom-pairs within hydrogen bonding distance? Thanks, Yao -- 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] Fw: g_hbond segmentation fault
-- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 2/10915Segmentation fault __ Hi guys, I got the msg like above when I ran g_hbond in version 4.5. Any guess on the problem? Thanks, Yao -- 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] Fw: g_hbond segmentation fault
Hi Erik, Sorry about that, I did not notice it. I used the command line, g_hbond -f test.trr -s test.tpr -ac test.xvg -e 100 -dt 1 Thanks, Yao --- On Tue, 9/28/10, Erik Marklund er...@xray.bmc.uu.se wrote: From: Erik Marklund er...@xray.bmc.uu.se Subject: Re: [gmx-users] Fw: g_hbond segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday, September 28, 2010, 6:22 PM Yao Yao skrev 2010-09-28 19.25: -- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 2/10915Segmentation fault __ Hi guys, I got the msg like above when I ran g_hbond in version 4.5. Any guess on the problem? Thanks, Yao And I replied and asked you what was the command line. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.se http://folding.bmc.uu.se/ -Inline Attachment Follows- -- 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_hbond segmentation fault
-- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 2/10915Segmentation fault __ Hi guys, I got the msg like above when I ran g_hbond in version 4.5. Any guess on the problem? Thanks, Yao -- 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] 4.5 Installation failure
Hi Gmxers, I was trying to install gmx 4.5 after installing the most recent fftw package in the same directory. Then I extracted gmx and ran ./configure and make, but it showed make: *** No targets specified and no makefile found. Stop. Anyone know what I did wrong? Thanks, Yao -- 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] Fw: NO GSL! Can't find and take away ballistic term in ACF without GSL
--- On Tue, 9/14/10, Yao Yao ya...@ymail.com wrote: Dear Gmxers, I met this msg when running g_hbond in 4.5-beta version. Then it gives Segmentation Fault without any time frame reading. Does anyone know what it means? thanks, Yao -- 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] NO GSL! Can't find and take away ballistic term in ACF without GSL
I met this msg when running g_hbond in 4.5-beta version. Then it gives Segmentation Fault without any time frame reading. Does anyone know what it means? -- 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] OWT5 not found in Charmmff
I am running tip5p in charmm force field in gmx. In energy minimization step, it gives an error msg as below. I just simply added it in atomtypes.atp in charmm27.ff, but still it doesn't work. Does anyone know how to solve it? Many thanks, Yao --- Program grompp, VERSION 4.5-beta3 Source code file: toppush.c, line: 1166 Fatal error: Atomtype OWT5 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- -- 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] tip5p.itp in Charmm
Hi, I am running charmmm force field (ff) in gmx 4.5 version and just trying on tip5p water model in it. Unfortunately I only find tip5p.gro is in the ff, not tip5p.itp file. Can anyone help me with hints on constructing it? Many thanks, Yao -- 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
