[gmx-users] Questions concerning autocorrealtion function
Hello! i)Here are the commands for my problem with the autocorrelation function which I mentioned in mails before: g_dist -f traj.trr -s topol.tpr -n index.ndx -o dist.xvg g_analyze -f dist.xvg -ac autocorr.xvg -P 2 Fatal error: Incompatible mode bits: normal and vector (or Legendre) What is the problem here? ii) Usually the rdfs are calculated until half the box length. How can I increase the distance range? Regards, Thomas -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de -- 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] specific heat
is there any command in gromacs that gives me a list of data points for specific heat and suseptibility as a function of temperature or time ? if not, then how can i calculate specific heat or polt Cv as a fuction of T? -- 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] specific heat
On 2011-01-30 11.43, leila separdar wrote: is there any command in gromacs that gives me a list of data points for specific heat and suseptibility as a function of temperature or time ? if not, then how can i calculate specific heat or polt Cv as a fuction of T? This is not trivial. You can compute the specific heat from fluctuations in the enthalpy or total energy: cP = (H^2 - H^2)/kB T^2 (NPT sim) cV = (Etot^2 - Etot^2)/kB T^2 (NVT sim) In addition you need to apply quantum corrections which are not negligible (see manual chapter 1). You can do this using a normal mode analysis. The implementation in released versions of g_energy is not correct, but as it happens I just committed a new version of g_energy and g_nmeig. If you download gromacs from git and checkout the release-4-5-patches branch everything should be there to compute cP/cV. Run g_nmeig -h for more information. As regards susceptibility, do you mean the dielectric constant? That can be computed using g_dipoles *from a trajectory* - not from an energy file anymore. -- 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.sehttp://folding.bmc.uu.se -- 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] PME parameter in GROMACS
Dear all, I would like to know if there is a way in GROMACS to find or specify the value of kappa (or Ewald coupling/splitting parameter) for the PME technique that we use in our simulation. In my case, I would like to perform simulations with a specified kappa value and a grid size of A x A x A for the PME parameter. If I understand it correctly, the grid can be specified by the following in GROMACS: fourier_nx = A, fourier_ny = 6, and fourier_nz = A. For the kappa, I could not find any information about it so far from the manual or our mailing list. Many thanks. Best regards, Aldi -- 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] PME parameter in GROMACS
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On 01/30/2011 01:18 PM, aldi asmadi wrote:
Dear all,
I would like to know if there is a way in GROMACS to find or specify the
value of kappa (or Ewald coupling/splitting parameter) for the PME
technique that we use in our simulation. In my case, I would like to
perform simulations with a specified kappa value and a grid size of A x
A x A for the PME parameter. If I understand it correctly, the grid can
be specified by the following in GROMACS: fourier_nx = A, fourier_ny =
6, and fourier_nz = A. For the kappa, I could not find any information
about it so far from the manual or our mailing list.
Many thanks.
Best regards,
Aldi
Unfortunately, Gromacs does not allow to input the splitting parameter
directly, however just a small change in src/gmxlib/ewald_util.c is
necessary to interpret a negative ewald_rtol in the mdp file as the
splitting parameter. Therefore add after the declaration of the
variables in calc_ewaldcoeff (line 53):
if (dtol0.0){
return -dtol;
}
If you are furthermore interested in an estimate of the error introduced
by your SPME parameters, try the tool g_pme_error, which also tells you
in the output file the corresponding splitting parameter \beta for a
certain cut-off and ewald_rtol. Together with g_tune_pme I have realized
that a quite remarkable gain in performance can be achieved, if the
tools are used hand in hand.
/Flo
- --
Florian Dommert
Dipl.-Phys.
Institute for Computational Physics
University Stuttgart
Pfaffenwaldring 27
70569 Stuttgart
Phone: +49(0)711/685-6-3613
Fax: +49-(0)711/685-6-3658
EMail: domm...@icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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Re: [gmx-users] energy minimization of a charged system in vacuum
On 29/01/11 05:08, Matt Chan wrote: Perfect. This is great reading. Thanks for the pointers Mark. Matt On 01/28/2011 06:50 PM, Mark Abraham wrote: On 29/01/2011 9:57 AM, Matthew Chan wrote: Hi, I'm a first time GROMACS user. I've got 2 questions, which I'll ask in separate emails. The first is about running EM on a charged protein in vacuum. I'm presently walking through some of the tutorials and trying to simplify them for my purposes. One is the energy minimization of the 1AKI lysozyme protein. I would like to minimize this protein in vacuum instead of solution as the tutorial demonstrates. Since the genion program replaces water molecules with ions to balance the charge of the system and there's no water, I'm having trouble running the simulation with a neutral system. My question is what effect does running a simulation with a charged system have? I recall reading that something related to PME calculations assumes the system is neutral, but it did not specify whether it was referring to MD or EM. From the mailing list, I have only been able to determine that running a charged system in solution makes no sense biologically. Some threads elsewhere cover these issues: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3976.html http://archive.ambermd.org/200712/0223.html Mark Since I have exactly the same needs (charged system in vacuum) I jump in... In http://www.gromacs.org/Documentation/Errors it says: Note for PME users: It is possible to use a uniform neutralizing background charge in PME to compensate for a system with a net background charge. There is probably nothing wrong with this in principle, because the uniform charge will not perturb the dynamics. From the reading above, it seems that namd/amber implementations already *implicitly* use this kind of compensation by ignoring terms in the summation. Is it the same for GROMACS? thanks, M. -- Massimo Sandal, Ph.D. http://devicerandom.org -- 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] energy minimization of a charged system in vacuum
On 2011-01-30 16.02, ms wrote: On 29/01/11 05:08, Matt Chan wrote: Perfect. This is great reading. Thanks for the pointers Mark. Matt On 01/28/2011 06:50 PM, Mark Abraham wrote: On 29/01/2011 9:57 AM, Matthew Chan wrote: Hi, I'm a first time GROMACS user. I've got 2 questions, which I'll ask in separate emails. The first is about running EM on a charged protein in vacuum. I'm presently walking through some of the tutorials and trying to simplify them for my purposes. One is the energy minimization of the 1AKI lysozyme protein. I would like to minimize this protein in vacuum instead of solution as the tutorial demonstrates. Since the genion program replaces water molecules with ions to balance the charge of the system and there's no water, I'm having trouble running the simulation with a neutral system. My question is what effect does running a simulation with a charged system have? I recall reading that something related to PME calculations assumes the system is neutral, but it did not specify whether it was referring to MD or EM. From the mailing list, I have only been able to determine that running a charged system in solution makes no sense biologically. Some threads elsewhere cover these issues: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3976.html http://archive.ambermd.org/200712/0223.html Mark Since I have exactly the same needs (charged system in vacuum) I jump in... In http://www.gromacs.org/Documentation/Errors it says: Note for PME users: It is possible to use a uniform neutralizing background charge in PME to compensate for a system with a net background charge. There is probably nothing wrong with this in principle, because the uniform charge will not perturb the dynamics. I'd like to comment that, this is tricky business. If your charges are spread out homogeneously it may be OK, but in practice this is often not the case (e.g. side chains on a protein). One should try to avoid this if at all possible. From the reading above, it seems that namd/amber implementations already *implicitly* use this kind of compensation by ignoring terms in the summation. Is it the same for GROMACS? thanks, M. Gromacs does not ignore any terms in the simulations if I am not mistaken. It also computes PME at every step in contrast to NAMD (don't know about Amber). -- 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.sehttp://folding.bmc.uu.se -- 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] energy minimization of a charged system in vacuum
On 30/01/11 15:41, David van der Spoel wrote: My question is what effect does running a simulation with a charged system have? I recall reading that something related to PME calculations assumes the system is neutral, but it did not specify whether it was referring to MD or EM. From the mailing list, I have only been able to determine that running a charged system in solution makes no sense biologically. Some threads elsewhere cover these issues: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3976.html http://archive.ambermd.org/200712/0223.html Mark Since I have exactly the same needs (charged system in vacuum) I jump in... In http://www.gromacs.org/Documentation/Errors it says: Note for PME users: It is possible to use a uniform neutralizing background charge in PME to compensate for a system with a net background charge. There is probably nothing wrong with this in principle, because the uniform charge will not perturb the dynamics. I'd like to comment that, this is tricky business. If your charges are spread out homogeneously it may be OK, but in practice this is often not the case (e.g. side chains on a protein). One should try to avoid this if at all possible. Oh, this is very bad news. Could you elaborate on that? (I have a CG model where this would be badly needed). Can spreading neutralizing charges along the other chain atoms be a viable alternative for enough atoms and enough low charge? (e.g. if I have 100 atoms and a +5 net charge, adding a -0.05 charge on all others?) From the reading above, it seems that namd/amber implementations already *implicitly* use this kind of compensation by ignoring terms in the summation. Is it the same for GROMACS? thanks, M. Gromacs does not ignore any terms in the simulations if I am not mistaken. It also computes PME at every step in contrast to NAMD (don't know about Amber). Thanks. m. -- Massimo Sandal, Ph.D. http://devicerandom.org -- 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] energy minimization of a charged system in vacuum
On 2011-01-30 17.08, ms wrote: On 30/01/11 15:41, David van der Spoel wrote: My question is what effect does running a simulation with a charged system have? I recall reading that something related to PME calculations assumes the system is neutral, but it did not specify whether it was referring to MD or EM. From the mailing list, I have only been able to determine that running a charged system in solution makes no sense biologically. Some threads elsewhere cover these issues: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3976.html http://archive.ambermd.org/200712/0223.html Mark Since I have exactly the same needs (charged system in vacuum) I jump in... In http://www.gromacs.org/Documentation/Errors it says: Note for PME users: It is possible to use a uniform neutralizing background charge in PME to compensate for a system with a net background charge. There is probably nothing wrong with this in principle, because the uniform charge will not perturb the dynamics. I'd like to comment that, this is tricky business. If your charges are spread out homogeneously it may be OK, but in practice this is often not the case (e.g. side chains on a protein). One should try to avoid this if at all possible. Oh, this is very bad news. Could you elaborate on that? (I have a CG model where this would be badly needed). With homogeneous I mean a solution of ions. Can spreading neutralizing charges along the other chain atoms be a viable alternative for enough atoms and enough low charge? (e.g. if I have 100 atoms and a +5 net charge, adding a -0.05 charge on all others?) Sounds like a recipe for disaster. Try looking for solutions with explicit counter ions. From the reading above, it seems that namd/amber implementations already *implicitly* use this kind of compensation by ignoring terms in the summation. Is it the same for GROMACS? thanks, M. Gromacs does not ignore any terms in the simulations if I am not mistaken. It also computes PME at every step in contrast to NAMD (don't know about Amber). Thanks. m. -- 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.sehttp://folding.bmc.uu.se -- 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] ngmx doesnot work; CH3-CH2-OH
Hi Everyone, Program ngmx, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/tpxio.c, line: 1708 Fatal error: reading tpx file (md1.tpr) version 73 with version 58 program I installed 4.0.7 before, and now i installed 4.5.3. How can i use ngmx now? The second question is running C2H5OH (ethanol). It should be 9 atoms per molecule. But i download the .top using PRDUG, the C2H5OH has 4 atoms. So i can still run, but some H atoms are ingored. Is it still no 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
Re: [gmx-users] ngmx doesnot work; CH3-CH2-OH
gromacs wrote: Hi Everyone, Program ngmx, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/tpxio.c, line: 1708 Fatal error: reading tpx file (md1.tpr) version 73 with version 58 program I installed 4.0.7 before, and now i installed 4.5.3. How can i use ngmx now? You need a compatible .tpr file, i.e. one generated with version 4.5.3, otherwise you have to use a 4.0.7 .tpr file with the 4.0.7 version of ngmx. Higher versions can read older file formats, but the reverse is generally not true. The second question is running C2H5OH (ethanol). It should be 9 atoms per molecule. But i download the .top using PRDUG, the C2H5OH has 4 atoms. So i can still run, but some H atoms are ingored. Is it still no problem? PRODRG produces united-atom topologies for the Gromos96 force fields. If you need or want a different force field, you need to build a suitable topology by some other method. -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] ngmx doesnot work; CH3-CH2-OH
On 31/01/2011 11:15 AM, gromacs wrote: Hi Everyone, Program ngmx, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/tpxio.c, line: 1708 Fatal error: reading tpx file (md1.tpr) version 73 with version 58 program I installed 4.0.7 before, and now i installed 4.5.3. How can i use ngmx now? You haven't configured 4.5.3 to build ngmx, haven't installed it, or haven't arranged your path to use it. See http://www.gromacs.org/Downloads/Installation_Instructions The second question is running C2H5OH (ethanol). It should be 9 atoms per molecule. But i download the .top using PRDUG, the C2H5OH has 4 atoms. So i can still run, but some H atoms are ingored. Is it still no problem? If you ask for a united-atom representation, you usually get one. See http://www.gromacs.org/Downloads/Related_Software/PRODRG 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] ngmx doesnot work; CH3-CH2-OH
On 31/01/2011 11:34 AM, Justin A. Lemkul wrote: gromacs wrote: Hi Everyone, Program ngmx, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/tpxio.c, line: 1708 Fatal error: reading tpx file (md1.tpr) version 73 with version 58 program I installed 4.0.7 before, and now i installed 4.5.3. How can i use ngmx now? You need a compatible .tpr file, i.e. one generated with version 4.5.3, otherwise you have to use a 4.0.7 .tpr file with the 4.0.7 version of ngmx. Higher versions can read older file formats, but the reverse is generally not true. The OP is using 4.0.7 ngmx with 4.5.3 .tpr file. They have to use software that is at least as recent as their .tpr. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] luck
Hi everyone! I have two questions. 1. after I installed gromacs 4.5.3 and which mdrun was able to give the correct path, I was not able to run luck. Instead, luck gives an error command not found. Is this ok? What went wrong? Do I need to install again gromacs? 2. I tried doing pdb2gmx. The error points the structure file *.pdb as the error. Does this in dicate that the program was not installed properly or there is an error with the pdb file. Thanks -- 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] solvation_box_preparation
Please tell me where I am wrong. I downloaded pdb of chaps and used prodrg server to get .itp and .gro file. Then I checked .itp for any missing charge and I found it correct. Then I created 6.0x6.0x6.0 box with genbox inserting 7 molecules of chaps.gro. Then again using genbox and -maxsol I put 510 spc.itp in the box to get a density approaching 1. Then I did steepest descent energy minimization with constraints = none, for emtotal=2000 and emstep=3000. Up to this the gromacs runs fine. when I start simulated annealing for cooling at high pressure with constraint = all_bonds the programme gives fatal error linc warning and stops. If I do energy minimization with constraint =all_bonds then also with some error of linc wrning the minimization is completed. When I do minimization without adding water then there is no linc warning and minimization is completed but with final positive potential energy. Then as suggested by Justin I used smaller box and there also in simulated annealing stage the system gives linc warning and the programme stops with fatal error. Please tell me where I am wrong. shahid nayeem On Fri, Jan 28, 2011 at 10:59 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 28/01/2011 3:51 PM, shahid nayeem wrote: Thanks Justin I tried with new box size of 2.8x2.8x2.8 . During energy minimization with steepest descent to force of 2000 and constraint=none, the system converged in 754 steps with positive potential energy. In subsequent simulated annealing with constraint all bonds it starts giving link warning in 0 step with rms 7407.805164, max 66989.116545 (between atom 94 and 117) and a list of bond thar rotated more than 30 degree almost atom number belonging to chaps molecule. You've set up a system that isn't stable, but we don't have enough information to have any idea why. I tried with new box size doesn't go close to describing your method in enough detail for anyone to know where you went wrong. See http://www.gromacs.org/Documentation/Terminology/Blowing_Up for generic tips Mark Please help. shahid Nayeem On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkuljalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am sending this mail again on user list because my reply to Mark’s query was not uploaded on the list. Original messge: I am trying to prepare a solvation box of chaps. After generating .itp and .gro at ProDrg and thorough check of charges, I started with a box size of 6x6x6. Energy minimization, simulated annealing (Cooling under high pressure and again heating at normal pressure) as well as final equilibration ran smoothly. But finally I get a box where all water molecules get accumulated in two three small region within the box and all chaps molecules gets accumulated in another small regions.I wanted near random uniform distribution of chaps in water. Any help from user, where I am wrong and what should I do. Reply to query. I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox –ci 7 chaps.gro).Then I solvated the output box with genbox using -maxsol 500 and spc216.gro. On visualization, at this stage itself uniform solvation did not occur (I got water in one region and chaps molecule in other region) but I observed a similar situation while If your box was not completely solvated, then don't use -maxsol. A box of 6x6x6 nm should require more than 500 molecules of water to fill. If you're trying to achieve some specific mole fraction or concentration, then re-figure your box size. -Justin preparing 10M urea salvation box. This was followed by 1ns simulated annealing from temp 300K to 0K and pressure 100 bar, then 1ns simulated annealing from temp. 0k to 300k and then ins equilibriation at this temperature. In case of urea finally I got uniformly solvated urea_water_box but in chaps I couldn’t get it. Shahid Nayeem -- 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 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
Re: [gmx-users] luck
Mr Bernard Ramos wrote: Hi everyone! I have two questions. 1. after I installed gromacs 4.5.3 and which mdrun was able to give the correct path, I was not able to run luck. Instead, luck gives an error command not found. Is this ok? What went wrong? Do I need to install again gromacs? The program is now called g_luck. 2. I tried doing pdb2gmx. The error points the structure file *.pdb as the error. Does this in dicate that the program was not installed properly or there is an error with the pdb file. If the program has given you a fatal error, then the program is correctly installed and working. It is your input that is somehow wrong. Without the actual error message, it's impossible to say what's wrong. -Justin Thanks -- 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] solvation_box_preparation
shahid nayeem wrote: Please tell me where I am wrong. I downloaded pdb of chaps and used prodrg server to get .itp and .gro file. Then I checked .itp for any missing charge and I found it correct. Then I created 6.0x6.0x6.0 box PRODRG doesn't have a problem of missing charges. It provides notoriously incorrect charges. with genbox inserting 7 molecules of chaps.gro. Then again using genbox and -maxsol I put 510 spc.itp in the box to get a density approaching 1. Then I did steepest descent energy minimization with constraints = none, for emtotal=2000 and emstep=3000. Up to this the These settings make no sense. An emtol of 2000 is very high, and emstep of 3000 is total nonsense. How well did you EM converge? What were the values of the potential energy and maximum force? gromacs runs fine. when I start simulated annealing for cooling at high pressure with constraint = all_bonds the programme gives fatal error linc warning and stops. If I do energy minimization with constraint =all_bonds then also with some error of linc wrning the minimization is completed. When I do minimization without adding water then there is no linc warning and minimization is completed but with final positive potential energy. Then as suggested by Justin I used smaller box and there also in simulated annealing stage the system gives linc warning and the programme stops with fatal error. Please tell me where I am wrong. How about simplifying the problem. Does the system run under normal conditions? In other words, can you run normal MD? You're treating the system very harshly with the combination of high pressure and annealing. Without seeing your .mdp file for this process, it's impossible to say how reasonable your settings are. It is also possible that your parameters for CHAPS (if they are the default ones from PRODRG) are incorrect. The charges and charge groups nearly always are. Without seeing them, there's nothing better to offer. -Justin shahid nayeem On Fri, Jan 28, 2011 at 10:59 AM, Mark Abraham mark.abra...@anu.edu.au wrote: On 28/01/2011 3:51 PM, shahid nayeem wrote: Thanks Justin I tried with new box size of 2.8x2.8x2.8 . During energy minimization with steepest descent to force of 2000 and constraint=none, the system converged in 754 steps with positive potential energy. In subsequent simulated annealing with constraint all bonds it starts giving link warning in 0 step with rms 7407.805164, max 66989.116545 (between atom 94 and 117) and a list of bond thar rotated more than 30 degree almost atom number belonging to chaps molecule. You've set up a system that isn't stable, but we don't have enough information to have any idea why. I tried with new box size doesn't go close to describing your method in enough detail for anyone to know where you went wrong. See http://www.gromacs.org/Documentation/Terminology/Blowing_Up for generic tips Mark Please help. shahid Nayeem On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkuljalem...@vt.edu wrote: shahid nayeem wrote: Dear All I am sending this mail again on user list because my reply to Mark’s query was not uploaded on the list. Original messge: I am trying to prepare a solvation box of chaps. After generating .itp and .gro at ProDrg and thorough check of charges, I started with a box size of 6x6x6. Energy minimization, simulated annealing (Cooling under high pressure and again heating at normal pressure) as well as final equilibration ran smoothly. But finally I get a box where all water molecules get accumulated in two three small region within the box and all chaps molecules gets accumulated in another small regions.I wanted near random uniform distribution of chaps in water. Any help from user, where I am wrong and what should I do. Reply to query. I created a box of 6x6x6 inserting 7 molecule of chaps with (genbox –ci 7 chaps.gro).Then I solvated the output box with genbox using -maxsol 500 and spc216.gro. On visualization, at this stage itself uniform solvation did not occur (I got water in one region and chaps molecule in other region) but I observed a similar situation while If your box was not completely solvated, then don't use -maxsol. A box of 6x6x6 nm should require more than 500 molecules of water to fill. If you're trying to achieve some specific mole fraction or concentration, then re-figure your box size. -Justin preparing 10M urea salvation box. This was followed by 1ns simulated annealing from temp 300K to 0K and pressure 100 bar, then 1ns simulated annealing from temp. 0k to 300k and then ins equilibriation at this temperature. In case of urea finally I got uniformly solvated urea_water_box but in chaps I couldn’t get it. Shahid Nayeem -- 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
Re: [gmx-users] Monitoring the water movement during simulation
On 01/31/11, bharat gupta bharat.85.m...@gmail.com wrote: Hi, I am completed a 3 ns simulation of a 230 aa protein .. Now I want to check whether the water is entering the proteins and through which side of the protein .. Since the whole protein is surrounded by water I don't know how this can be done .. is there any command to check .. also I have tried doing it in VMD but there I am not able to do so ?? Use g_select to create index groups of waters within a known distance of a central point. Then look at those groups in VMD. Mark Pls help -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] luck
Do I need to type in g_luck instead? --- On Mon, 1/31/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] luck To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:11 PM Mr Bernard Ramos wrote: Hi everyone! I have two questions. 1. after I installed gromacs 4.5.3 and which mdrun was able to give the correct path, I was not able to run luck. Instead, luck gives an error command not found. Is this ok? What went wrong? Do I need to install again gromacs? The program is now called g_luck. 2. I tried doing pdb2gmx. The error points the structure file *.pdb as the error. Does this in dicate that the program was not installed properly or there is an error with the pdb file. If the program has given you a fatal error, then the program is correctly installed and working. It is your input that is somehow wrong. Without the actual error message, it's impossible to say what's wrong. -Justin Thanks -- 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] luck
Mr Bernard Ramos wrote: Do I need to type in g_luck instead? Typing an email and waiting for a response takes far more time and effort than simply trying it yourself ;) -Justin --- On *Mon, 1/31/11, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] luck To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:11 PM Mr Bernard Ramos wrote: Hi everyone! I have two questions. 1. after I installed gromacs 4.5.3 and which mdrun was able to give the correct path, I was not able to run luck. Instead, luck gives an error command not found. Is this ok? What went wrong? Do I need to install again gromacs? The program is now called g_luck. 2. I tried doing pdb2gmx. The error points the structure file *.pdb as the error. Does this in dicate that the program was not installed properly or there is an error with the pdb file. If the program has given you a fatal error, then the program is correctly installed and working. It is your input that is somehow wrong. Without the actual error message, it's impossible to say what's wrong. -Justin Thanks -- 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://us.mc527.mail.yahoo.com/mc/compose?to=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 http://us.mc527.mail.yahoo.com/mc/compose?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] luck
yup, i typed g_luck and it worked. the error that shows is -- File input/output error: filename.pdb For more information, visit -- --- On Mon, 1/31/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] luck To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:11 PM Mr Bernard Ramos wrote: Hi everyone! I have two questions. 1. after I installed gromacs 4.5.3 and which mdrun was able to give the correct path, I was not able to run luck. Instead, luck gives an error command not found. Is this ok? What went wrong? Do I need to install again gromacs? The program is now called g_luck. 2. I tried doing pdb2gmx. The error points the structure file *.pdb as the error. Does this in dicate that the program was not installed properly or there is an error with the pdb file. If the program has given you a fatal error, then the program is correctly installed and working. It is your input that is somehow wrong. Without the actual error message, it's impossible to say what's wrong. -Justin Thanks -- 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] luck
Mr Bernard Ramos wrote: yup, i typed g_luck and it worked. the error that shows is -- File input/output error: filename.pdb For more information, visit -- Then filename.pdb doesn't exist. You need to specify the actual name of your input .pdb file; filename.pdb is just a generic name that shows you how to use the program. -Justin --- On *Mon, 1/31/11, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] luck To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:11 PM Mr Bernard Ramos wrote: Hi everyone! I have two questions. 1. after I installed gromacs 4.5.3 and which mdrun was able to give the correct path, I was not able to run luck. Instead, luck gives an error command not found. Is this ok? What went wrong? Do I need to install again gromacs? The program is now called g_luck. 2. I tried doing pdb2gmx. The error points the structure file *.pdb as the error. Does this in dicate that the program was not installed properly or there is an error with the pdb file. If the program has given you a fatal error, then the program is correctly installed and working. It is your input that is somehow wrong. Without the actual error message, it's impossible to say what's wrong. -Justin Thanks -- 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://us.mc527.mail.yahoo.com/mc/compose?to=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 http://us.mc527.mail.yahoo.com/mc/compose?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] luck
thanks. Here is the error i mentioned a while back with using pdb2gmx: -- File input/output error: filename.pdb For more information, visit -- thanks for the time --- On Mon, 1/31/11, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] luck To: Gromacs Users' List gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:33 PM Mr Bernard Ramos wrote: Do I need to type in g_luck instead? Typing an email and waiting for a response takes far more time and effort than simply trying it yourself ;) -Justin --- On *Mon, 1/31/11, Justin A. Lemkul /jalem...@vt.edu/* wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] luck To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, January 31, 2011, 12:11 PM Mr Bernard Ramos wrote: Hi everyone! I have two questions. 1. after I installed gromacs 4.5.3 and which mdrun was able to give the correct path, I was not able to run luck. Instead, luck gives an error command not found. Is this ok? What went wrong? Do I need to install again gromacs? The program is now called g_luck. 2. I tried doing pdb2gmx. The error points the structure file *.pdb as the error. Does this in dicate that the program was not installed properly or there is an error with the pdb file. If the program has given you a fatal error, then the program is correctly installed and working. It is your input that is somehow wrong. Without the actual error message, it's impossible to say what's wrong. -Justin Thanks -- 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://us.mc527.mail.yahoo.com/mc/compose?to=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 http://us.mc527.mail.yahoo.com/mc/compose?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 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] Monitoring the water movement during simulation
I tracked the movement of water molecules around residues 65 to 67 of my protein (GFP crystal structure) .. According to the literature water should not enter the protein (reason being the cage like structure of GFP) .. but in VMD, 2 water molecules have been tracked to interact with chromophore ... So , I am a bit confused as it should not have happened ?? ... For my analysis I need to check whether the water is entering the protein or not .. Since I have simulated some variant structures (long loops) of GFP and I need to check how this structure would or would not lead to the entrance of water ?? On Sun, Jan 30, 2011 at 8:20 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 01/31/11, *bharat gupta * bharat.85.m...@gmail.com wrote: Hi, I am completed a 3 ns simulation of a 230 aa protein .. Now I want to check whether the water is entering the proteins and through which side of the protein .. Since the whole protein is surrounded by water I don't know how this can be done .. is there any command to check .. also I have tried doing it in VMD but there I am not able to do so ?? Use g_select to create index groups of waters within a known distance of a central point. Then look at those groups in VMD. Mark Pls help -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] 4.5.3 Installation under Cygwin
Hello, I am trying to install gromacs 4.5.3 on my desktop under Cygwin. Using the installation procedure from the Wiki: (http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO Install fftw-3.2.2 with ./configure --enable-sse --enable-float make make install Then install gromacs with: ./configure --enable-shared LDFLAGS='-L/usr/local/lib' make The installation fails here with many errors not being able to find libraries associated with fftw tracing back to this error: *** Warning: This system can not link to static lib archive /usr/local/lib/libfftw3f.la. *** I have the capability to make that library automatically link in when *** you link to this library. But I can only do this if you have a *** shared version of the library, which you do not appear to have. The installation procedure from the Wiki works fine with gromacs-4.0.7. This error only occurs with the 4.5 series. Are there different default settings for where gromacs looks for fftw between 4.0.7 and 4.5.3? Any help would be appreciated. Thanks, Mike -- 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] 4.5.3 Installation under Cygwin
On 01/31/11, toma0...@umn.edu wrote: Hello, I am trying to install gromacs 4.5.3 on my desktop under Cygwin. Using the installation procedure from the Wiki: (http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO Install fftw-3.2.2 with ./configure --enable-sse --enable-float make make install Then install gromacs with: ./configure --enable-shared LDFLAGS='-L/usr/local/lib' make The installation fails here with many errors not being able to find libraries associated with fftw tracing back to this error: *** Warning: This system can not link to static lib archive /usr/local/lib/libfftw3f.la. *** I have the capability to make that library automatically link in when *** you link to this library. But I can only do this if you have a *** shared version of the library, which you do not appear to have. The installation procedure from the Wiki works fine with gromacs-4.0.7. This error only occurs with the 4.5 series. Are there different default settings for where gromacs looks for fftw between 4.0.7 and 4.5.3? Any help would be appreciated. I ran into the same issue a while back. I don't know what causes it. I found that using a CMake-based build on Cygwin worked. 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: Fwd: [gmx-users] Monitoring the water movement during simulation
On 01/31/11, bharat gupta bharat.85.m...@gmail.com wrote: -- Forwarded message -- From: bharat gupta bharat.85.m...@gmail.com Date: Sun, Jan 30, 2011 at 9:30 PM Subject: Re: [gmx-users] Monitoring the water movement during simulation To: Discussion list for GROMACS users gmx-users@gromacs.org I tracked the movement of water molecules around residues 65 to 67 of my protein (GFP crystal structure) .. According to the literature water should not enter the protein (reason being the cage like structure of GFP) .. but in VMD, 2 water molecules have been tracked to interact with chromophore ... So , I am a bit confused as it should not have happened ?? We can't tell. We don't know if your simulation model is flawed, the literature is wrong, your modified GFP do let water in, or your observations of interacting with the chromophore aren't right. ... For my analysis I need to check whether the water is entering the protein or not .. Since I have simulated some variant structures (long loops) of GFP and I need to check how this structure would or would not lead to the entrance of water ?? To observe a transit, look for snapshots where they were in one place, and snapshots where they were in another. Mark On Sun, Jan 30, 2011 at 8:20 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 01/31/11, bharat gupta bharat.85.m...@gmail.com wrote: Hi, I am completed a 3 ns simulation of a 230 aa protein .. Now I want to check whether the water is entering the proteins and through which side of the protein .. Since the whole protein is surrounded by water I don't know how this can be done .. is there any command to check .. also I have tried doing it in VMD but there I am not able to do so ?? Use g_select to create index groups of waters within a known distance of a central point. Then look at those groups in VMD. Mark Pls help -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- 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 -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Fwd: GROMACS user: error with pdb2gmx
I am not a free private GROMACS help service. Please direct correspondence to the users list. Please consider the advice here before doing so http://www.gromacs.org/Support Mark ---BeginMessage--- Hi Mark! Sorry to bother you. I am new to gromacs. I tried using pdb2gmx. However, after running it, i get this error message and no new files are created by pdb2gmx. It says Reading filename.pdb -- File input/output error: filename.pdb For more information, visit -- It failed reading the input file. the file was a pdb file modified using Avogadro, i also tried saving it again using Vega ZZ. please help. what seems to be the error. thanks Bernard ---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
Re: Fwd: [gmx-users] Monitoring the water movement during simulation
I followed the lysozyme tutorial step by step and everything seems to be fine and the literature cannot be wrong as it has been proved .. I have repeated this simulation second time... I want to ask one thing that during solvation step and equilibration step water is mixed with the protein so it means that the structure should not have water inside it during equilibration step itself or not ? On Sun, Jan 30, 2011 at 10:34 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 01/31/11, *bharat gupta * bharat.85.m...@gmail.com wrote: -- Forwarded message -- From: bharat gupta bharat.85.m...@gmail.com Date: Sun, Jan 30, 2011 at 9:30 PM Subject: Re: [gmx-users] Monitoring the water movement during simulation To: Discussion list for GROMACS users gmx-users@gromacs.org I tracked the movement of water molecules around residues 65 to 67 of my protein (GFP crystal structure) .. According to the literature water should not enter the protein (reason being the cage like structure of GFP) .. but in VMD, 2 water molecules have been tracked to interact with chromophore ... So , I am a bit confused as it should not have happened ?? We can't tell. We don't know if your simulation model is flawed, the literature is wrong, your modified GFP do let water in, or your observations of interacting with the chromophore aren't right. ... For my analysis I need to check whether the water is entering the protein or not .. Since I have simulated some variant structures (long loops) of GFP and I need to check how this structure would or would not lead to the entrance of water ?? To observe a transit, look for snapshots where they were in one place, and snapshots where they were in another. Mark On Sun, Jan 30, 2011 at 8:20 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 01/31/11, *bharat gupta * bharat.85.m...@gmail.com wrote: Hi, I am completed a 3 ns simulation of a 230 aa protein .. Now I want to check whether the water is entering the proteins and through which side of the protein .. Since the whole protein is surrounded by water I don't know how this can be done .. is there any command to check .. also I have tried doing it in VMD but there I am not able to do so ?? Use g_select to create index groups of waters within a known distance of a central point. Then look at those groups in VMD. Mark Pls help -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: Fwd: [gmx-users] Monitoring the water movement during simulation
I followed the lysozyme tutorial step by step and everything seems to be fine and the literature cannot be wrong as it has been proved .. I have repeated this simulation second time... I want to ask one thing that during solvation step and equilibration step water is mixed with the protein so it means that the structure should not have water inside it during equilibration step itself or not ? On Sun, Jan 30, 2011 at 10:50 PM, bharat gupta bharat.85.m...@gmail.comwrote: I followed the lysozyme tutorial step by step and everything seems to be fine and the literature cannot be wrong as it has been proved .. I have repeated this simulation second time... I want to ask one thing that during solvation step and equilibration step water is mixed with the protein so it means that the structure should not have water inside it during equilibration step itself or not ? On Sun, Jan 30, 2011 at 10:34 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 01/31/11, *bharat gupta * bharat.85.m...@gmail.com wrote: -- Forwarded message -- From: bharat gupta bharat.85.m...@gmail.com Date: Sun, Jan 30, 2011 at 9:30 PM Subject: Re: [gmx-users] Monitoring the water movement during simulation To: Discussion list for GROMACS users gmx-users@gromacs.org I tracked the movement of water molecules around residues 65 to 67 of my protein (GFP crystal structure) .. According to the literature water should not enter the protein (reason being the cage like structure of GFP) .. but in VMD, 2 water molecules have been tracked to interact with chromophore ... So , I am a bit confused as it should not have happened ?? We can't tell. We don't know if your simulation model is flawed, the literature is wrong, your modified GFP do let water in, or your observations of interacting with the chromophore aren't right. ... For my analysis I need to check whether the water is entering the protein or not .. Since I have simulated some variant structures (long loops) of GFP and I need to check how this structure would or would not lead to the entrance of water ?? To observe a transit, look for snapshots where they were in one place, and snapshots where they were in another. Mark On Sun, Jan 30, 2011 at 8:20 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 01/31/11, *bharat gupta * bharat.85.m...@gmail.com wrote: Hi, I am completed a 3 ns simulation of a 230 aa protein .. Now I want to check whether the water is entering the proteins and through which side of the protein .. Since the whole protein is surrounded by water I don't know how this can be done .. is there any command to check .. also I have tried doing it in VMD but there I am not able to do so ?? Use g_select to create index groups of waters within a known distance of a central point. Then look at those groups in VMD. Mark Pls help -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor
Re: Fwd: [gmx-users] Monitoring the water movement during simulation
On 01/31/11, bharat gupta bharat.85.m...@gmail.com wrote: I followed the lysozyme tutorial step by step and everything seems to be fine and the literature cannot be wrong as it has been proved .. Is your model of the chromophore reasonable? IIRC forming the chromophore requires making some new bonds. I have repeated this simulation second time... If you don't tell us how you assessed 2 water molecules have been tracked to interact with chromophore in such a way that somebody could (in principle) repeat it, then we'll just assume you've done it wrongly. I called g_select with these inputs to make an index file, then used editconf like this with that index file to make a subset structure and loaded that in VMD to compare with the original structure, and saw this is a method. Then you asked how to see whether the loops were letting water in. If there were waters interacting with the chromophore, then it seems you've proved they were letting water in. But that hinges on whether we believe your previous statements :-) I want to ask one thing that during solvation step and equilibration step water is mixed with the protein so it means that the structure should not have water inside it during equilibration step itself or not ? Read genbox -h Mark On Sun, Jan 30, 2011 at 10:34 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 01/31/11, bharat gupta bharat.85.m...@gmail.com wrote: -- Forwarded message -- From: bharat gupta bharat.85.m...@gmail.com Date: Sun, Jan 30, 2011 at 9:30 PM Subject: Re: [gmx-users] Monitoring the water movement during simulation To: Discussion list for GROMACS users gmx-users@gromacs.org I tracked the movement of water molecules around residues 65 to 67 of my protein (GFP crystal structure) .. According to the literature water should not enter the protein (reason being the cage like structure of GFP) .. but in VMD, 2 water molecules have been tracked to interact with chromophore ... So , I am a bit confused as it should not have happened ?? We can't tell. We don't know if your simulation model is flawed, the literature is wrong, your modified GFP do let water in, or your observations of interacting with the chromophore aren't right. ... For my analysis I need to check whether the water is entering the protein or not .. Since I have simulated some variant structures (long loops) of GFP and I need to check how this structure would or would not lead to the entrance of water ?? To observe a transit, look for snapshots where they were in one place, and snapshots where they were in another. Mark On Sun, Jan 30, 2011 at 8:20 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 01/31/11, bharat gupta bharat.85.m...@gmail.com wrote: Hi, I am completed a 3 ns simulation of a 230 aa protein .. Now I want to check whether the water is entering the proteins and through which side of the protein .. Since the whole protein is surrounded by water I don't know how this can be done .. is there any command to check .. also I have tried doing it in VMD but there I am not able to do so ?? Use g_select to create index groups of waters within a known distance of a central point. Then look at those groups in VMD. Mark Pls help -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- 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 -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- Bharat
Re: Fwd: [gmx-users] Monitoring the water movement during simulation
I selected the water molecules but using atom selection in VMD by using the following command water and within 5 of resid 65 to 67, 65 to 67 is the chromophore position ... some 2 or 3 water molecules were found near to the chromophore i.e. inside the beta barrel ... Practically it should not happen .. Also I checked the structure that I saved after genbox command .. and I found some 3 water molecules inside the barrel .. After reading about genbox .. what I understood is that it solvates the protein in specified solvent ... but still i donot understand whether during solvation step the water will go inside the barrel or not ... pls help as its a bit confusing ?? On Sun, Jan 30, 2011 at 11:40 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 01/31/11, *bharat gupta * bharat.85.m...@gmail.com wrote: I followed the lysozyme tutorial step by step and everything seems to be fine and the literature cannot be wrong as it has been proved .. Is your model of the chromophore reasonable? IIRC forming the chromophore requires making some new bonds. I have repeated this simulation second time... If you don't tell us how you assessed 2 water molecules have been tracked to interact with chromophore in such a way that somebody could (in principle) repeat it, then we'll just assume you've done it wrongly. I called g_select with these inputs to make an index file, then used editconf like this with that index file to make a subset structure and loaded that in VMD to compare with the original structure, and saw this is a method. Then you asked how to see whether the loops were letting water in. If there were waters interacting with the chromophore, then it seems you've proved they were letting water in. But that hinges on whether we believe your previous statements :-) I want to ask one thing that during solvation step and equilibration step water is mixed with the protein so it means that the structure should not have water inside it during equilibration step itself or not ? Read genbox -h Mark On Sun, Jan 30, 2011 at 10:34 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 01/31/11, *bharat gupta * bharat.85.m...@gmail.com wrote: -- Forwarded message -- From: bharat gupta bharat.85.m...@gmail.com Date: Sun, Jan 30, 2011 at 9:30 PM Subject: Re: [gmx-users] Monitoring the water movement during simulation To: Discussion list for GROMACS users gmx-users@gromacs.org I tracked the movement of water molecules around residues 65 to 67 of my protein (GFP crystal structure) .. According to the literature water should not enter the protein (reason being the cage like structure of GFP) .. but in VMD, 2 water molecules have been tracked to interact with chromophore ... So , I am a bit confused as it should not have happened ?? We can't tell. We don't know if your simulation model is flawed, the literature is wrong, your modified GFP do let water in, or your observations of interacting with the chromophore aren't right. ... For my analysis I need to check whether the water is entering the protein or not .. Since I have simulated some variant structures (long loops) of GFP and I need to check how this structure would or would not lead to the entrance of water ?? To observe a transit, look for snapshots where they were in one place, and snapshots where they were in another. Mark On Sun, Jan 30, 2011 at 8:20 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 01/31/11, *bharat gupta * bharat.85.m...@gmail.com wrote: Hi, I am completed a 3 ns simulation of a 230 aa protein .. Now I want to check whether the water is entering the proteins and through which side of the protein .. Since the whole protein is surrounded by water I don't know how this can be done .. is there any command to check .. also I have tried doing it in VMD but there I am not able to do so ?? Use g_select to create index groups of waters within a known distance of a central point. Then look at those groups in VMD. Mark Pls help -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. -
