[gmx-users] simulation single molecule in water
Dear gromacs users, I'm simulating a single molecule in spc water. I'm using a cubic water box which has 3.4 nm size. I got the toplogy of my molecule via PRODRG. After running minimization, NVT , NPT and MD for 10 ns , I checked the density of water ,it was less than the real value (1000 kg m\S-3\N) ,actually I got around 950. I have checked my mdp file in the NPT step and I was wondering about tau_p that I should use. First I used 2.0 ps with Parrinello-Rahman coupling. After checking in gromacs archive, I found it is better to use 0.5 ps, I have changed tau-p ,but I still have density value less than 1000. Details of my mdp file are below : Run parameters integrator= md; leap-frog integrator nsteps= 500; 2 * 500 = 1 ps, 1 ns dt= 0.002; 2 fs ; Output control nstxout= 1000; save coordinates every 2 ps nstvout= 1000; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 2 ps nstenergy= 1000; save energies every 2 ps nstlog= 1000; update log file every 2 ps ; Bond parameters continuation= yes; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= system; two coupling groups - more accurate tau_t= 0.1; time constant, in ps ref_t= 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= isotropic; uniform scaling of box vectors tau_p= 0.50; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= no; Velocity generation is off What should be the origin of this density difference? looking forward to your advise -- 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] simulation single molecule in water
It would be better if you run it a bit longer than 10ns and check the density again. But it is not a big problem I guess as the density of water at 300K should not be exactly 1000kg/m^3. Its ~1000kg/m^3 at 277K. do not expect to get exactly real value :) Additionally your system is not purely water molecules in a box there is a small molecule in it which might have an effect on the density. Cheers, -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Souilem Safa Sent: Tuesday, 7 May 2013 4:38 PM To: Discussion list for GROMACS users Subject: [gmx-users] simulation single molecule in water Dear gromacs users, I'm simulating a single molecule in spc water. I'm using a cubic water box which has 3.4 nm size. I got the toplogy of my molecule via PRODRG. After running minimization, NVT , NPT and MD for 10 ns , I checked the density of water ,it was less than the real value (1000 kg m\S-3\N) ,actually I got around 950. I have checked my mdp file in the NPT step and I was wondering about tau_p that I should use. First I used 2.0 ps with Parrinello-Rahman coupling. After checking in gromacs archive, I found it is better to use 0.5 ps, I have changed tau-p ,but I still have density value less than 1000. Details of my mdp file are below : Run parameters integrator= md; leap-frog integrator nsteps= 500; 2 * 500 = 1 ps, 1 ns dt= 0.002; 2 fs ; Output control nstxout= 1000; save coordinates every 2 ps nstvout= 1000; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 2 ps nstenergy= 1000; save energies every 2 ps nstlog= 1000; update log file every 2 ps ; Bond parameters continuation= yes; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= system; two coupling groups - more accurate tau_t= 0.1; time constant, in ps ref_t= 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= isotropic; uniform scaling of box vectors tau_p= 0.50; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= no; Velocity generation is off What should be the origin of this density difference? looking forward to your advise -- 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] Usage of g_spatial
Dear gromacs users, I am analyzing trajectories of an ionic liquid system generated using AMBER MD package. The force field parameters are typical of this IL system and not from the existing libraries. Hence, it is difficult for me to generate a tpr file. I understand that running the g_spatial command needs pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I need tpr file for that. So there is no way of doing g_spatial without a tpr file is it? Then how do I generate tpr file for my system? Thanks for all the help -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] Usage of g_spatial
I think you can process the trajectories without generating TPR. Dr. Vitaly Chaban On Tue, May 7, 2013 at 12:12 PM, Venkat Reddy venkat...@gmail.com wrote: Dear gromacs users, I am analyzing trajectories of an ionic liquid system generated using AMBER MD package. The force field parameters are typical of this IL system and not from the existing libraries. Hence, it is difficult for me to generate a tpr file. I understand that running the g_spatial command needs pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I need tpr file for that. So there is no way of doing g_spatial without a tpr file is it? Then how do I generate tpr file for my system? Thanks for all the help -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] simulation single molecule in water
Your problem has nothing to do with barostat. There is such thing as DispCorr. I am unsure whether if should be turned on or off in case of your model. It does influence density to certain extent. Dr. Vitaly Chaban -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Souilem Safa Sent: Tuesday, 7 May 2013 4:38 PM To: Discussion list for GROMACS users Subject: [gmx-users] simulation single molecule in water Dear gromacs users, I'm simulating a single molecule in spc water. I'm using a cubic water box which has 3.4 nm size. I got the toplogy of my molecule via PRODRG. After running minimization, NVT , NPT and MD for 10 ns , I checked the density of water ,it was less than the real value (1000 kg m\S-3\N) ,actually I got around 950. I have checked my mdp file in the NPT step and I was wondering about tau_p that I should use. First I used 2.0 ps with Parrinello-Rahman coupling. After checking in gromacs archive, I found it is better to use 0.5 ps, I have changed tau-p ,but I still have density value less than 1000. Details of my mdp file are below : Run parameters integrator= md; leap-frog integrator nsteps= 500; 2 * 500 = 1 ps, 1 ns dt= 0.002; 2 fs ; Output control nstxout= 1000; save coordinates every 2 ps nstvout= 1000; save velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory output every 2 ps nstenergy= 1000; save energies every 2 ps nstlog= 1000; update log file every 2 ps ; Bond parameters continuation= yes; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= system; two coupling groups - more accurate tau_t= 0.1; time constant, in ps ref_t= 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= isotropic; uniform scaling of box vectors tau_p= 0.50; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= no; Velocity generation is off What should be the origin of this density difference? looking forward to your advise -- 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
Aw: Re: [gmx-users] Proteins with ADP ATP cofactors
That works, wish you could choose more force fields in the anti-chamber as a plugin. Theres some auxillary scripts also for martini and gromos force fields to .psf but they were mostly for the ff19, so partial atom. They antichamber is probably easier, and if you get something in ff19 (or better 22 as an all atom) you just have to add a few missing hydrogens for the first, etc...the problem I had was the naming schemes go from simple numbers (listed say as angles 1-4-3) to deffinitions, (CA-C-H) so easy to make mistakes... Stephan Watkins Gesendet:Dienstag, 07. Mai 2013 um 01:03 Uhr Von:micheal j twin michealj.t...@gmail.com An:gmx-users@gromacs.org Betreff:Re: [gmx-users] Proteins with ADP ATP cofactors Dear Stephan, thank you for your reply. Im performing some test with antechamber for a de-novo parametrization, hope to see some good results with it. You probably have to do a hand job. Look at the .itp/top files and then the force field parmeters, heres not many atoms, so it would take only a couple hours. -- 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 dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant 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] FW: Myristic Acid Simulations
Hi, I know there have been many threads talking about parameterization of novel molecules for simulations within gromacs, but I just wanted to know if anyone had done any parameterization of myristic acid, as I intend to begin simulations on a protein that is myristolated and figured I'd check here before embarking on what sounds like it will be a very long and confusing process for a parameterization-newbie. I found a paper in which they've used myristic acid within their simulations (Ariel Alvarez et al., 2012, J.Biophys. http://www.hindawi.com/journals/jbp/2012/642745/) however they've only listed the topology coordinates of this molecule. Is it possible to create a .rtp from this topology? Would this require parameterization based on the force field I am using? If so where would I find information on the bond angles and dihedrals for this? Any advice on creating a .rtp file would be greatly appreciated!! Thanks Natalie -- 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:
http://brotherauto.sakura.ne.jp/xcwylh.php -- 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] mdrun-gpu error message on Gromacs 4.5.5
On 5/6/13 9:39 PM, Andrew DeYoung wrote: Hi, I am running mdrun-gpu on Gromacs 4.5.5 (with OpenMM). This is my first time using a GPU. I get the following error message when attempting to run mdrun-gpu with my .tpr file: --- Program mdrun-gpu, VERSION 4.5.5 Source code file: /usr/local/src/gromacs-4.5.5/src/kernel/openmm_wrapper.cpp, line: 1365 Fatal error: OpenMM exception caught while initializating: getPropertyValue: Illegal property name For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I get this error when calling with: mdrun-gpu -s topol.tpr and with: mdrun-gpu -device OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=no -s topol.tpr I can't seem to find this particular error message in the documentation or previously discussed on this mailing list. Does this error message suggest that I am calling mdrun-gpu incorrectly, or that OpenMM is improperly installed? It looks to be a rather generic OpenMM error message, which unfortunately isn't very helpful. I got lots of those, along with random failures, that led me to abandon using OpenMM within Gromacs. Support for OpenMM in Gromacs is limited at best, as OpenMM is being deprecated. Is there any reason you're not using the native GPU support from 4.6.1? The only reason to try to use OpenMM is for GPU-accelerated implicit solvent simulations, so if that's what you're doing I can understand. Otherwise, use 4.6.1. -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
Re: [gmx-users] center of mass and box co-ordinates
On 5/7/13 1:05 AM, Arunima Shilpi wrote: Hello Justin sir In your tutorial file for umbrella sampling for Aβ42 protofibril, what was the criteria used to determine the coordinates of center of mass and box size which you have takes as editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560 4.362 12 The protein complex is centered in x and y, and the z-dimension provides sufficient space to allow for pulling of 5 nm. -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
Re: [gmx-users] FW: Myristic Acid Simulations
On 5/7/13 6:40 AM, Natalie Stephenson wrote: Hi, I know there have been many threads talking about parameterization of novel molecules for simulations within gromacs, but I just wanted to know if anyone had done any parameterization of myristic acid, as I intend to begin simulations on a protein that is myristolated and figured I'd check here before embarking on what sounds like it will be a very long and confusing process for a parameterization-newbie. I found a paper in which they've used myristic acid within their simulations (Ariel Alvarez et al., 2012, J.Biophys. http://www.hindawi.com/journals/jbp/2012/642745/) however they've only listed the topology coordinates of this molecule. Is it possible to create a .rtp from this topology? Would this require parameterization based on the force field I am using? If so where would I find information on the bond angles and dihedrals for this? The nice part about Gromos96 parameter sets is that they're designed to be transferrable, i.e. you can build molecules piecewise from constituent functional groups. Doing so usually gives you a reasonable topology. You will have to adjust how the carboxylate is treated, since you don't have free myristic acid, but presumably some other covalent linkage to the protein. I also wonder why those authors used 43A1; the lipid parameters in that set were rather poor, and alkanes were reparameterized in a later revision of Gromos96. You can certainly create an .rtp entry from the listed topology. See Chapter 5 of the manual for details. Bonded parameters are easy to introduce. All that pdb2gmx requires is a [bonds] directive in the .rtp, and it figures out the angles and dihedrals based on the bonds. Whether or not suitable bonded parameters can then be applied is something you will have to check, but for a simple acyl chain there should be no problem. Again, 43A1 may be a poor choice, though, and you should consider a newer parameter set. -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] cudaStreamSynchronize failed
Hello, I am running a bilayer simulation with Gromacs4.6.1. I have just bought the GPU card and I am doing some tests with a DPPC bilayer simulation. But I am always getting the same error: --- Program mdrun, VERSION 4.6.1 Source code file: /home/cintia/Downloads/gromacs-4.6.1/src/mdlib/nbnxn_cuda/nbnxn_cuda.cu, line: 565 Fatal error: cudaStreamSynchronize failed in cu_blockwait_nb: unspecified launch failure For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I saw that someone posted a similar error here before, but I was not able to understand the solution for it. Can anyone help? Below is the .log file with the details of the hardware and the system. Thank you in advance, Cíntia Log file opened on Mon May 6 21:19:32 2013 Host: titan2 pid: 12346 nodeid: 0 nnodes: 1 Gromacs version:VERSION 4.6.1 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:enabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: SSE4.1 FFT library:fftw-3.3.2-sse2 Large file support: enabled RDTSCP usage: enabled Built on: Sex Mai 3 16:52:44 BRT 2013 Built by: root@titan2 [CMAKE] Build OS/arch: Linux 3.8.0-19-generic x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Core(TM) i7 CPU 870 @ 2.93GHz Build CPU family: 6 Model: 30 Stepping: 5 Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 C compiler: /usr/bin/cc GNU cc (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3 C compiler flags: -msse4.1 -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU c++ (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3 C++ compiler flags: -msse4.1 -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG CUDA compiler: nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2012 NVIDIA Corporation;Built on Fri_Sep_21_17:28:58_PDT_2012;Cuda compilation tools, release 5.0, V0.2.1221 CUDA driver:5.50 CUDA runtime: 5.0 :-) G R O M A C S (-: God Rules Over Mankind, Animals, Cosmos and Such :-) VERSION 4.6.1 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) mdrun (-: PLEASE READ AND CITE THE FOLLOWING REFERENCE B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 --- Thank You --- Input Parameters: integrator = md
[gmx-users] Usage of g_spatial
Try this: trjconv -s my.pdb -f my.pdb -o mymod.pdb g_spatial -s mymod.pdb -f mymod.pdb For the pre-processing, there must also be AMBER tools that will do this for you if for some reason the above does not work for you (e.g. Option -pbc mol requires a .tpr file for the -s option) Chris. -- original message -- I am analyzing trajectories of an ionic liquid system generated using AMBER MD package. The force field parameters are typical of this IL system and not from the existing libraries. Hence, it is difficult for me to generate a tpr file. I understand that running the g_spatial command needs pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I need tpr file for that. So there is no way of doing g_spatial without a tpr file is it? Then how do I generate tpr file for my system? Thanks for all the help -- -- 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] Usage of g_spatial
Sorry for my ignorance, since the help manual uses tpr file for the first two steps before running g_spatial, could you please tell me how I should do them without tpr. Also when I just run g_spatial (without the first two steps) I get the distribution of all the anions around cations, so it is not informative. Thank you so much for all the help On Tue, May 7, 2013 at 2:48 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: I think you can process the trajectories without generating TPR. Dr. Vitaly Chaban On Tue, May 7, 2013 at 12:12 PM, Venkat Reddy venkat...@gmail.com wrote: Dear gromacs users, I am analyzing trajectories of an ionic liquid system generated using AMBER MD package. The force field parameters are typical of this IL system and not from the existing libraries. Hence, it is difficult for me to generate a tpr file. I understand that running the g_spatial command needs pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I need tpr file for that. So there is no way of doing g_spatial without a tpr file is it? Then how do I generate tpr file for my system? Thanks for all the help -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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 -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] Periodic Boundary Condition in evaporation of droplets
Dear All, I just had a question regarding using the PBC for evaporation of clusters. Due to PBC the evaporated molecules again come back to drop (re-condensation). For me such a process is physically meaning less. Shall I ask a question from GMX users about this issue. How we can eliminated this unphysical process? Please ote that I'm not interest to use vacuum since vapour pressure of nanodrop is essential foR my MD simulation. Many thanks Rasoul -- 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] issue in replica exchange
These symptoms sound a lot like a bug I reported back in 2010: http://redmine.gromacs.org/issues/433 - closed with only a short comment from Berk that it was fixed for 4.5. With my fix as detailed in the redmine report I've been happily doing NPT replica exchange with my custom code forked from 4.0.5 - I've never tested any later versions. The key point there was that the problem only occurred with one CPU per replica - I'm afraid I haven't gone through this whole thread, have you tested both single and multiple CPUs per replica? - Original Message - From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Thursday, 2 May 2013, 11:53 Subject: Re: [gmx-users] issue in replica exchange On Wed, May 1, 2013 at 10:24 PM, XAvier Periole x.peri...@rug.nl wrote: Ok here is my current status on that REMD issue. For info: I use Temperature: v-rescale, tau_t = 2.0 ps Pressure: berendsen, tau_p = 5.0 ps, time step: dt=0.002 - 0.020 fs, COM removal on for bilayer/water separately The symptoms: explosion of the system after 2-5 steps following the swap, first sign is a huge jump in LJ interactions and pressure. This jump seems to be absorbed by the box size and temperature when possible … see example I provided earlier. A large VCM (velocity centre of mass?) is often associated with the crash. But also pressure scaling more than 1% ... 1- the problem mentioned above remains in gmx-4.5.7 and it might actually got worse. I was able to run a 500 ns simulation with gmx405 using similar setup as for gmx457. The following point happened in gmx457. 2- it persists with a time step of 2 fs. Actually all tests performed in the following used dt=2fs. 3- if I perform an exchange that explodes within mdrun myself (externally to the remd gromacs by getting the gro file with the mdp adjusting the temperature) it goes all fine. 4- the issue gets much worst when the consecutive replicas differ (different protein conformations and the box size etc) … explosion at first exchange. 5- the use of parrinelo-raman does not help 6- cancelling the centre of mass removal does not remove the problem. 7- switching to NVT ensemble does not help but makes it worst (crash in 2 steps). All exchanges accepted at first attempt crash with the message Large VCM(group SOL): -0.0XXX , -0.XXX, -0.16XXX, Temp-cm:6.55XXX 8- using a unique conformation (the same) for all replicas in the NVT REMD simulation after equilibration in the same NVT ensemble (for 1 ns) removes the problem. 9- taking the equilibrated NVT conformations, equilibrate them in an NPT ensemble (1 ns) and let go the exchanges afterwards restores the problem … one exchange is not properly done at the second trial, while the first ones were fine. Well if errors were made that was with reasonable 10- note also that the coarse grain I use is extremely forgiving, meaning you can perform really nasty transformations and run it further after simple minimisation … so even abrupt changes in temperatures should be fine and relax quickly. 11- when looking at the conformations themselves nothing appears to have jumped over or nothing funky. At this point I am not sure what to think and what to do next. There is definitely something not going right during the exchanges. OK, thanks for the effort. That all agrees with my suspicion that the full state is not being exchanged. Anyone has been able to run a REMD simulation in an NPT ensemble without crashes? I would imagine someone has and something particular to my system is making it going wrong but I am really wondering what it could be. My feeling is that something relative to the box size or pressure is not going across but it might be something completely different, when the consecutive systems differ reasonably. I've never tried, but an experiment with a water box might be instructive. However that would suggest that the manner the exchanges are made is severely wrong in some cases. Any help to resolve the problem would be greatly appreciated. There is an outstanding REMD issue on redmine that could be related ( http://redmine.gromacs.org/issues/1191). I'd suggest you open a new issue there, upload a minimal set of .tprs that can reproduce the problem and anything you can think of that might help investigate. For something I'm doing, I'd like to be sure the full T-coupling state is being exchanged, and we may as well kill all the bugs at once. Mark XAvier. On Apr 26, 2013, at 9:21 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, Apr 25, 2013 at 11:05 PM, XAvier Periole x.peri...@rug.nl wrote: Thanks for the answer. I'll check gmx4.5.7 and report back. I am not sure what you mean by GROMACS swaps the coordinates not the ensemble data. The coupling to P and T and not exchanged with it? The code in src/kernel/repl_ex.c: static void exchange_state(const gmx_multisim_t *ms, int
[gmx-users] ionic liquids - viscosity via green kubo relation
Hello all, I have a periodic system of composed of 200 pairs of 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl)imide. I equilibrate the system for 1.5 ns to the appropriate density under 1 atm and 300 K in the NPT ensemble. As a sidenote, I do obtain the density cited in the literature for the system and force field in question. Once equilibrated, I pass into the NVE ensemble, and store the the Pxy pressure tensor component of the entire group of atoms. I am doing this to calculate the viscosity of my liquid using the Green-Kubo relation. I have been calculating the Stress Autocorrelation Function (SACF) for Pxy using Matlab. The autocorrelation window is 4 ps, and data was stored over a 1 ns production run every 5 fs (200 000 data points). I know a 1 ns run may be slightly short for an ionic liquid, but the simulations take quite a long time already, and I therefore wanted to rule out any other issues before doing a longer run. The SACF (normalized to 1) that I obtain is attached, and I do not really know what to make of it; it is not smooth at all (quite jaggedy in fact!). Furthermore, when I integrate to compute the viscosity (I do not integrate the normalized curve obviously), I obtain around 6 cP which is 2 orders of magnitude too small... I am quite sure there are no errors in the parameters of my force field, maybe someone can suggest something that I may have missed? -- 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] ionic liquids - viscosity via green kubo relation
Hello, I would try to extend ACF window (10, 50, 200ps) but not too much since you might end with integrating noise which would lead to overestimation of viscosity. For water, 4ps seems to be ok but your liquid might have longer ACF tail so you are actually getting seriously underestimated viscosity. You should also run calculations for Pxz, Pyz, (Pxx-Pyy)/2 and (Pyy-Pzz)/2 to improve statistics. Regards, km. On Tue, May 7, 2013 at 4:13 PM, Thomas P tomas...@gmail.com wrote: Hello all, I have a periodic system of composed of 200 pairs of 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl)imide. I equilibrate the system for 1.5 ns to the appropriate density under 1 atm and 300 K in the NPT ensemble. As a sidenote, I do obtain the density cited in the literature for the system and force field in question. Once equilibrated, I pass into the NVE ensemble, and store the the Pxy pressure tensor component of the entire group of atoms. I am doing this to calculate the viscosity of my liquid using the Green-Kubo relation. I have been calculating the Stress Autocorrelation Function (SACF) for Pxy using Matlab. The autocorrelation window is 4 ps, and data was stored over a 1 ns production run every 5 fs (200 000 data points). I know a 1 ns run may be slightly short for an ionic liquid, but the simulations take quite a long time already, and I therefore wanted to rule out any other issues before doing a longer run. The SACF (normalized to 1) that I obtain is attached, and I do not really know what to make of it; it is not smooth at all (quite jaggedy in fact!). Furthermore, when I integrate to compute the viscosity (I do not integrate the normalized curve obviously), I obtain around 6 cP which is 2 orders of magnitude too small... I am quite sure there are no errors in the parameters of my force field, maybe someone can suggest something that I may have missed? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Periodic Boundary Condition in evaporation of droplets
If you don't want to simulate your droplet in a perfect vacuum then in most MD codes you have to use either PBC or walls. There are advantages and disadvantages to both. I'm not an expert but in my opinion PBC make more physical sense than walls provided the box is sensibly chosen, *however*, I am not an expert. I suggest that you consult the literature for a discussion of the merits of various boundary conditions for MD simulations of droplets. There will be many papers discussing it and I'd be shocked if there aren't several review articles as well. Richard On 07/05/13 14:50, Rasoul Nasiri wrote: Dear All, I just had a question regarding using the PBC for evaporation of clusters. Due to PBC the evaporated molecules again come back to drop (re-condensation). For me such a process is physically meaning less. Shall I ask a question from GMX users about this issue. How we can eliminated this unphysical process? Please ote that I'm not interest to use vacuum since vapour pressure of nanodrop is essential foR my MD simulation. Many thanks Rasoul -- 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] Periodic Boundary Condition in evaporation of droplets
Dear Richard, Thanks for your reply and comments. To be honest, I have read the couple of papers about the evaporation of droplets using PBC. There are controversial discussions on this question how to evaluate size of box so that PBC issue can be eliminated. While some author believe that size of box should be at least 10 times larger than diameter of drop, others think that this size is not important when system reached to quasi-equilibrium stage. Could you please let me know your idea about the sensible size of the box when PBC is applied? I would be appreciated if you could introduce me a recent review about it? Best wishes Rasoul On Tue, May 7, 2013 at 5:24 PM, Richard Broadbent richard.broadben...@imperial.ac.uk wrote: If you don't want to simulate your droplet in a perfect vacuum then in most MD codes you have to use either PBC or walls. There are advantages and disadvantages to both. I'm not an expert but in my opinion PBC make more physical sense than walls provided the box is sensibly chosen, *however*, I am not an expert. I suggest that you consult the literature for a discussion of the merits of various boundary conditions for MD simulations of droplets. There will be many papers discussing it and I'd be shocked if there aren't several review articles as well. Richard On 07/05/13 14:50, Rasoul Nasiri wrote: Dear All, I just had a question regarding using the PBC for evaporation of clusters. Due to PBC the evaporated molecules again come back to drop (re-condensation). For me such a process is physically meaning less. Shall I ask a question from GMX users about this issue. How we can eliminated this unphysical process? Please ote that I'm not interest to use vacuum since vapour pressure of nanodrop is essential foR my MD simulation. Many thanks Rasoul -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] Atomtype C not found
Hi I have been using the lipids from Prof Tieleman's website and (using Berger Lipids) in gromacs 4.5.4 I want to try the grompp tool but have encountered this problem: Fatal error: Atomtype C not found Topology file is as the following: #include lipid.itp #include dopc.itp #include spc.itp #include ions.itp '[ system ]' ; name DOPC bilayer in water '[ molecules ]' ; name number DOPC 128 SOL 4825 lipid.itpis as the following: [ defaults ] 1 1 [ atomtypes ] ;name mass charge ptype c6 c12 LO 15.9994 0.000 A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS LOM 15.9994 0.000 A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS LNL 14.0067 0.000 A 3.35300e-03 3.95100e-06 ;Nitrogen, OPLS LC 12.0110 0.000 A 4.88800e-03 1.35900e-05 ;Carbonyl C, OPLS LH1 13.0190 0.000 A 4.03100e-03 1.21400e-05 ;CH1, OPLS LH2 14.0270 0.000 A 7.00200e-03 2.48300e-05 ;CH2, OPLS … DOPC.itpisas the following: [ moleculetype ] ; Name nrexcl DOPC 3 [ atoms ] ; nr type resnr residu atom cgnr charge mass 1 LC3 1 DOPC C1 0 0.4000 15.0350 ; qtot:0.36 2 LC3 1 DOPC C2 0 0.4000 15.0350 ; qtot:0.72 3 LC3 1 DOPC C3 0 0.4000 15.0350 ; qtot:1.08 4 LNL 1 DOPC N4 0 -0.5000 14.0067 ; qtot:0.76 5 LH2 1 DOPC C5 0 0.3000 14.0270 ; qtot:1.0 6 LC2 1 DOPC C6 1 0.4000 14.0270 ; qtot:1.0 .. DOPC.grofile as the following: 128 DOPC in water 21387 1DOPC C1 1 4.048 0.461 2.197 -0.4628 -0.6241 -0.6552 1DOPC C2 2 4.064 0.596 2.395 -0.1879 0.0104 -0.0154 1DOPC C3 3 4.110 0.366 2.405 -0.5498 -0.8024 -0.0627 1DOPC N4 4 4.022 0.466 2.341 0.5789 -0.0490 -0.4766 1DOPC C5 5 3.877 0.457 2.361 0.5625 0.0560 -0.5460 1DOPC C6 6 3.823 0.315 2.343 0.0671 0.1818 -0.0962 ….. Many thanks for your help in advance! Sun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] a program to calculate the adsorbed molecules
Dear gmx users I would like to calculate the number of the surfactant molecules adsorbed on the nanotube surface as a function of time. I would be pleased if anyone could tell me whether there is a program in gromacs to do that or not? regards -- 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] Atomtype C not found
On 5/7/13 1:04 PM, Sun Moon wrote: Hi I have been using the lipids from Prof Tieleman's website and (using Berger Lipids) in gromacs 4.5.4 I want to try the grompp tool but have encountered this problem: Fatal error: Atomtype C not found This atomtype belongs to protein functional groups. In lipid.itp, nonbonded parameters are defined for protein-lipid interactions. If you do not need any protein-specific terms, delete that section of lipid.itp. -Justin Topology file is as the following: #include lipid.itp #include dopc.itp #include spc.itp #include ions.itp '[ system ]' ; name DOPC bilayer in water '[ molecules ]' ; name number DOPC 128 SOL 4825 lipid.itpis as the following: [ defaults ] 1 1 [ atomtypes ] ;name mass charge ptype c6 c12 LO15.99940.000 A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS LOM15.99940.000 A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS LNL14.00670.000 A 3.35300e-03 3.95100e-06 ;Nitrogen, OPLS LC12.01100.000 A 4.88800e-03 1.35900e-05 ;Carbonyl C, OPLS LH113.01900.000 A 4.03100e-03 1.21400e-05 ;CH1, OPLS LH214.02700.000 A 7.00200e-03 2.48300e-05 ;CH2, OPLS … DOPC.itpisas the following: [ moleculetype ] ; Name nrexcl DOPC 3 [ atoms ] ; nrtype resnr residuatomcgnrcharge mass 1 LC3 1DOPC C1 0 0.4000 15.0350 ; qtot:0.36 2 LC3 1DOPC C2 0 0.4000 15.0350 ; qtot:0.72 3 LC3 1DOPC C3 0 0.4000 15.0350 ; qtot:1.08 4 LNL 1DOPC N4 0-0.5000 14.0067 ; qtot:0.76 5 LH2 1DOPC C5 0 0.3000 14.0270 ; qtot:1.0 6 LC2 1DOPC C6 1 0.4000 14.0270 ; qtot:1.0 .. DOPC.grofile as the following: 128 DOPC in water 21387 1DOPCC11 4.048 0.461 2.197 -0.4628 -0.6241 -0.6552 1DOPCC22 4.064 0.596 2.395 -0.1879 0.0104 -0.0154 1DOPCC33 4.110 0.366 2.405 -0.5498 -0.8024 -0.0627 1DOPCN44 4.022 0.466 2.341 0.5789 -0.0490 -0.4766 1DOPCC55 3.877 0.457 2.361 0.5625 0.0560 -0.5460 1DOPCC66 3.823 0.315 2.343 0.0671 0.1818 -0.0962 ….. Many thanks for your help in advance! Sun -- 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
Re: [gmx-users] a program to calculate the adsorbed molecules
On 5/7/13 2:04 PM, Za Pour wrote: Dear gmx users I would like to calculate the number of the surfactant molecules adsorbed on the nanotube surface as a function of time. I would be pleased if anyone could tell me whether there is a program in gromacs to do that or not? Not directly, but perhaps you can integrate an RDF if designed cleverly. Otherwise, you'll have to script calls to g_dist or g_mindist with whatever adsorption criteria you have established for each molecule and count the frames in which the criteria are satisfied. -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
Re: [gmx-users] unstable system
Hi, I have run a new npt after energy minimization on my system composed of water/protein/lipid/ions. After a few nanoseconds for NPT, I ran MD, and got fatal error : X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group What is written in md.log file shows an improper pressure, Step Time Lambda 0 0.0 0.0 Energies (kJ/mol) U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 8.26284e+04 5.54129e+04 7.43891e+02 -1.96405e+02 8.37087e+03 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.05973e+05 8.51736e+04 -5.79669e+03 -1.11865e+06 -2.67464e+05 Position Rest. Potential Kinetic En. Total Energy Temperature 2.09408e+03 -1.26366e+06 3.33724e+05 -9.29932e+05 4.44648e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -1.09245e+02 -2.40668e+04 6.65938e-04 I' d like to know if it means that more that the system is required of more npt equilibration? Thanks for your suggestion. Please help me. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, April 19, 2013 11:29 PM Subject: Re: [gmx-users] unstable system On 4/19/13 2:57 PM, Shima Arasteh wrote: Thanks so much for your replies. I appreciate you. Do you think that more NPT equilibration might solve the problem? or wont work? I have no idea at what point you are in your procedure that is crashing. I'm not going to make some blind assessment of do more NPT or some random thing. If you just completed the EM as you posted, proceed with whatever equilibration protocol you believe to be sufficient. There is no one single answer here. If you're jumping straight into MD after the EM you showed, you need to start your equilibration over again completely. -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] equilibration of the simulated systems
Dear gmx users would you please tell me how I can be sure that my simulation time is long enough? is it appropriate way to use g_energy program and calculate total energy ? thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] equilibration of the simulated systems
yes. you can use g_energy to plot what you need (T, density or whatever) and decide if it is acceptable or not. In the latter case you simply have to extend your run (see http://www.gromacs.org/Documentation/How-tos/Extending_Simulations) cheers Francesco On Tue, 7 May 2013, at 06:58 PM, Za Pour wrote: Dear gmx users would you please tell me how I can be sure that my simulation time is long enough? is it appropriate way to use g_energy program and calculate total energy ? thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Francesco frac...@myopera.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] unstable system
On 5/7/13 2:42 PM, Shima Arasteh wrote: Hi, I have run a new npt after energy minimization on my system composed of water/protein/lipid/ions. After a few nanoseconds for NPT, I ran MD, and got fatal error : X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group What is written in md.log file shows an improper pressure, Step Time Lambda 00.00.0 Energies (kJ/mol) U-BProper Dih. Improper Dih. CMAP Dih. LJ-14 8.26284e+045.54129e+047.43891e+02 -1.96405e+028.37087e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. -1.05973e+058.51736e+04 -5.79669e+03 -1.11865e+06 -2.67464e+05 Position Rest. PotentialKinetic En. Total EnergyTemperature 2.09408e+03 -1.26366e+063.33724e+05 -9.29932e+05 4.44648e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -1.09245e+02 -2.40668e+046.65938e-04 I' d like to know if it means that more that the system is required of more npt equilibration? Thanks for your suggestion. Please help me. There is no reason why NPT should run stably but MD would then fail. The high initial temperature suggests that atoms are overlapping somehow or that the previous state has not been preserved properly. Please provide exact details of what you are doing, including the following: 1. Exact commands given in the preparation protocol (EM and equilibration) 2. The .mdp files being used for all steps, most importantly NPT and MD 3. Your grompp and mdrun invocations for the failing MD run -Justin - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, April 19, 2013 11:29 PM Subject: Re: [gmx-users] unstable system On 4/19/13 2:57 PM, Shima Arasteh wrote: Thanks so much for your replies. I appreciate you. Do you think that more NPT equilibration might solve the problem? or wont work? I have no idea at what point you are in your procedure that is crashing. I'm not going to make some blind assessment of do more NPT or some random thing. If you just completed the EM as you posted, proceed with whatever equilibration protocol you believe to be sufficient. There is no one single answer here. If you're jumping straight into MD after the EM you showed, you need to start your equilibration over again completely. -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 -- 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
RE: [gmx-users] equilibration of the simulated systems
That really depends on what property it is that you are interested in observing. You need to observe the dynamics of the property of interest, see over what time frames it changes, then ensure that you simulation time is enough to cover it equilibrating or changing. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Za Pour Sent: Wednesday, 8 May 2013 4:58 AM To: gmx-users@gromacs.org Subject: [gmx-users] equilibration of the simulated systems Dear gmx users would you please tell me how I can be sure that my simulation time is long enough? is it appropriate way to use g_energy program and calculate total energy ? thank you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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] Usage of g_spatial
See my previous response. You don't need a .tpr for trjconv (unless you are doing pbc operations). trjconv -h will also tell you that. Just use trjconv -s my.pdb Chris. -- original message -- Sorry for my ignorance, since the help manual uses tpr file for the first two steps before running g_spatial, could you please tell me how I should do them without tpr. Also when I just run g_spatial (without the first two steps) I get the distribution of all the anions around cations, so it is not informative. Thank you so much for all the help -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] error in running perl distance.pl
Hello sir While runnimg command for perl distance.pl in umbrella sampling it gives the following error Use of uninitialized value $distance in concatenation (.) or string at distance.pl line 30. readline() on closed filehandle IN at distance.pl line 16. Can you guide me in rectifying the error -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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] PCA_RMS fluctuation per residue?
Dear gmx users, I've done covariance matrix for backbone of protein using g_covar command. Also, can able to plot all projections through g_anaeig. However, I could only able to do -rmsf: plot the RMS fluctuation per atom of eigenvectors BUT i wants to do them per residue? How can i achieve this? In manual it shows -filt: command filter the trajectory to show only the motion along eigenvectors. How i do visualize this kind of motions? Rajiv -- 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
