Re: [gmx-users] TI results
parto haghighi wrote: Dear GMX users, I want to prepare an .itp for a new molecule ( like fifth gromacs tutorial). 1 ) I applied PRODRG to create its drg.itp. 2 ) Now I want to correct its partial atomic charge. As I have red in a paper (http://pubs.acs.org/doi/abs/10.1021/ci100335w) I have to do thermodynamic integration for example solvation free energy of this molecule in water to correct its charges. The molecule is lidocain My question is how can I accept my free energy calculation results while I dont have any experimental date to comparison? When it becomes clear that the free energy of solvation itself is not a quantity to which you can compare, you need something else. One such option that we have used in the past is comparing logP values (see our paper at http://pubs.acs.org/doi/abs/10.1021/bi1000855). For a drug molecule, finding a logP value should be trivial ;) -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problem with access to Gromacs after installation
Hello, I installed Gromacs 4.5.5 by Cygwin, then I can not get access to GROMACS after installation. With cygwin I installed this packets: perl, utils, devel, libs, math and system . Then I done everything what is wrote in instructions. Please help Sylwia Chmielewska -- 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] Intel composer vs. Intel Studio
Gromacs users, Please let me know what is the best option for gromacs compilation (looking for better performance in INFINIBAND QDR systems) 1. Intel composer XE i.e. Intel compilers, mkl but open MPI library 2. Intel studio i.e. Intel compilers, mkl, and Intel MPI library If there are any better options please let me know. Thanks in advance. new year greeting Sudip Disclaimer: This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory, Pune, India. You may review the policy at http://www.ncl-india.org/common/webmailDisclaimer.htm -- 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] exploding system
Hi, I met a very untamed simulation system. when I tried to run a short MD, it's collapsed with LINCS Warnings, It's under 317K so I used energy minimizations after NVT, and run another NVT_2 again. (In vacuum, no NPT being applied here). after that NVT_2, mainly increased the steps, run MD, it's collapsed again after 500ps, so I used the energy minimization from that nvt_2.gro several times, and it's collapsed during energy minimizations. Might I used wrong way of handling it. I tried 300K, which can run a bit further without collapse. Thanks for any suggestions you may give. Do I need to work hard on the energy minimization or? Best 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
[gmx-users] TI results
Dear GMX users, I want to prepare an .itp for a new molecule ( like fifth gromacs tutorial). 1 ) I applied PRODRG to create its drg.itp. 2 ) Now I want to correct its partial atomic charge. As I have red in a paper (http://pubs.acs.org/doi/abs/10.1021/ci100335w) I have to do thermodynamic integration for example solvation free energy of this molecule in water to correct its charges. The molecule is lidocain My question is how can I accept my free energy calculation results while I dont have any experimental date to comparison? Thanks a lot in advance. P.Haghighi -- 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] exploding system
On 12/27/2011 7:44 PM, lina wrote: Hi, I met a very untamed simulation system. when I tried to run a short MD, it's collapsed with LINCS Warnings, It's under 317K so I used energy minimizations after NVT, and run another NVT_2 again. (In vacuum, no NPT being applied here). after that NVT_2, mainly increased the steps, run MD, it's collapsed again after 500ps, so I used the energy minimization from that nvt_2.gro several times, and it's collapsed during energy minimizations. Might I used wrong way of handling it. I tried 300K, which can run a bit further without collapse. Thanks for any suggestions you may give. Do I need to work hard on the energy minimization or? The usual advice is here http://www.gromacs.org/Documentation/Terminology/Blowing_Up http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System. Mark -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] Intel composer vs. Intel Studio
On 12/27/2011 11:18 PM, Sudip Roy wrote: Gromacs users, Please let me know what is the best option for gromacs compilation (looking for better performance in INFINIBAND QDR systems) 1. Intel composer XE i.e. Intel compilers, mkl but open MPI library 2. Intel studio i.e. Intel compilers, mkl, and Intel MPI library GROMACS is strongly CPU-bound in a way that is rather insensitive to compilers and libraries. I would expect no strong difference between the above two - and icc+MKL+OpenMPI was only a few percent faster than gcc+FFTW+OpenMPI when I tested them on such a machine about two years ago. Mark -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] SPC density
Dear all I am starting some MD simulations aimed to calculate the volume of a solute in water as a function of the concentration. First I ran a simulation of a box with 4124 SPC water molecules (similar number of molecules that will be later used with my solute) for which I got the following results after ~7.5 ns: Statistics over 3762001 steps [ 0. thru 7524.0005 ps ], 3 data sets All averages are exact over 3762001 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 298125.156125.156 1.9202e-05 0.144476 Volume 126.90853.291753.2917 5.61522e-06 0.0422489 Density (SI)972.142408.201408.201 -4.30887e-05 -0.324199 Heat Capacity Cv: 16.9588 J/mol K (factor = 0.176389) Isothermal Compressibility: 0.543909 /bar Adiabatic bulk modulus:1.83854 bar Why am I obtaining so low density? The density seems to be constant over that timescale. This is my mdp file: constraints = all-bonds integrator = md dt = 0.002 nsteps = 250 nstxout = 5000 nstvout = 5 nstenergy = 1000 nstxtcout = 5000 energygrps = SOL nstlist = 5 ns_type = grid rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 coulombtype = PME fourierspacing = 0.15 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes Tcoupl = nose-hoover tau_t = 0.1 tc-grps = SOL ref_t = 298 Pcoupl = Parrinello-Rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 pcoupltype = isotropic gen_vel = yes gen_temp= 298 gen_seed= -1 Thanks in advance for any 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] problem with access to Gromacs after installation
On 12/27/2011 11:01 PM, Sylwia Chmielewska wrote: Hello, I installed Gromacs 4.5.5 by Cygwin, then I can not get access to GROMACS after installation. With cygwin I installed this packets: perl, utils, devel, libs, math and system . Then I done everything what is wrote in instructions. Those instructions presumably advised you to check with the standard installation instructions, which have the advice here: http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation Mark -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_angle calculation
On Wed, Dec 21, 2011 at 18:44, SebastianWaltz sebastian.wa...@physik.uni-freiburg.de wrote: Hi all, I try to reproduce the results from g_angle using my own c++ code. Using the formula θ=acos(r_ij * r_kj/|r_ij||r_kj|) with the acos from the cmath library, I obtain an angle which is always ~5% larger when the angel calculated by g_angle. Does g_angle use the same formula or does it calculate θ in a different way? The angles are calculated through src/gmxlib/bondfree.c::bond_angle() which does (after taking care of PBC): *costh=cos_angle(r_ij,r_kj); th=acos(*costh); cos_angle() is defined in include/vec.h to do r_ij * r_kj/|r_ij||r_kj|; acos() comes from the math lib, it's not a GROMACS function. So it's essentially what you seem to do. I guess approximations and precision loss might play a role, f.e. cos_angle() uses GROMACS' own gmx_invsqrt() - do you use math lib sqrt() to calculate the vector norm ? You could try cut-and-pasting the few pieces of code making up the GROMACS implementation of these functions - they are well contained in include/vec.h. Cheers, Bogdan -- 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] (no subject)
On 12/27/2011 5:38 PM, Nidhi Katyal wrote: Dear all, I am trying to create tmao box.Energy minimization, simulated annealing (Cooling under high pressure and again heating at normal pressure) as well as final equilibration ran smoothly. But finally I got a box where all water molecules got accumulated in two three small region within the box and tmao molecules in another small regions.I wanted near random uniform distribution of tmao in water. Perhaps the box didn't get equilibrated properly. Any help from user, where I am wrong and what should I do. Your SA protocol sounds like a recipe for problems. See http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation The usual process for generating a box of mixed solvents is here http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents but your cosolvent may be too large for the genbox -ci replacement procedure. Then, you may need to use the ideas here (http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation) to make a suitably dilute TMAO solution that can then be solvated with water with genbox -cs. Either way, lengthy equilibration will be in order. Mark -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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] SPC density
On 2011-12-27 17:57, Theodora García wrote: Dear all I am starting some MD simulations aimed to calculate the volume of a solute in water as a function of the concentration. First I ran a simulation of a box with 4124 SPC water molecules (similar number of molecules that will be later used with my solute) for which I got the following results after ~7.5 ns: dispcorr = enerpres Statistics over 3762001 steps [ 0. thru 7524.0005 ps ], 3 data sets All averages are exact over 3762001 steps Energy Average RMSD Fluct. Drift Tot-Drift --- Temperature 298125.156125.156 1.9202e-05 0.144476 Volume 126.90853.291753.2917 5.61522e-06 0.0422489 Density (SI)972.142408.201408.201 -4.30887e-05 -0.324199 Heat Capacity Cv: 16.9588 J/mol K (factor = 0.176389) Isothermal Compressibility: 0.543909 /bar Adiabatic bulk modulus:1.83854 bar Why am I obtaining so low density? The density seems to be constant over that timescale. This is my mdp file: constraints = all-bonds integrator = md dt = 0.002 nsteps = 250 nstxout = 5000 nstvout = 5 nstenergy = 1000 nstxtcout = 5000 energygrps = SOL nstlist = 5 ns_type = grid rlist = 1.2 rcoulomb= 1.2 rvdw= 1.2 coulombtype = PME fourierspacing = 0.15 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes Tcoupl = nose-hoover tau_t = 0.1 tc-grps = SOL ref_t = 298 Pcoupl = Parrinello-Rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 pcoupltype = isotropic gen_vel = yes gen_temp= 298 gen_seed= -1 Thanks in advance for any help... -- 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] trjconv and g_clustsize
Thank you very much from your reply. I found out that my problem is at step c (-pbc nojump) because I exercised ngmx after steps a and b by: ngmx -f cluster.gro -s cluster.tpr and I viewed 2 micelles the same of result of md.trr (or md.xtc). I studied http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions according to your advice and I think that I should Extract the first frame from the trajectory as reference for removing jumps and then Remove jumps according step c, but I have a problem about this! May I ask you to check my steps, please? 1- trjconv -f md.xtc -s md.tpr -o cluster.gro -e 60 -pbc cluster (and I selected 2 surfactants for clustering group and 0 system for outpup group) 2- grompp -f md.mdp -c cluster.gro -o cluster.tpr -n index.ndx Then I did: ngmx -f cluster.gro -s cluster.tpr and I viewed 2 micelles. 3- trjconv -f cluster.gro -s cluster.tpr -dump 0 -o clusterdump.gro (and I selected 0 system for output group) 4- grompp -f md.mdp -c clusterdump.gro -o cluster1.tpr -n index.ndx 5- trjconv -f cluster.gro -s cluster1.tpr -pbc nojump -o clusternojump.xtc Then I did: ngmx -f clusternojump.xtc -s cluster1.tpr and I had the same previous problem. May I ask you to help me, please? Best Regards Sara From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, December 26, 2011 4:20 PM Subject: Re: [gmx-users] trjconv and g_clustsize On 12/26/2011 7:53 PM, mohammad agha wrote: Dear Prof. I have several questions about trjconv, please help me. In my simulation is created 2 micelles. 1- When I do 3 steps of micelle clustering as follows: a- trjconv -f md.xtc -o a_cluster.gro-e 60 -pbc cluster b- grompp -f md.mdp -c a_cluster.gro -o a_cluster.tpr c- trjconv -f md.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump I view 2 micelles according to result of my simulation in VMD but in ngmx isn't view 2 micelles but just is view 1 micelle and reminder of monomers are collected in several groups in different places. So you don't have a single cluster of atoms... so as trjconv -h notes, using -pbc cluster isn't very useful when you don't have a cluster of atoms. All my advice of two days ago on this point still applies. Is it right if my criterion be view in VMD and is my micelle clustering correct? It's correct if it looks the way you want it to. 2- If I select surfactants for clustering group and system for output group in step (a) and I select system for output group in step (c), command g_clustsize doesn't work correct, consequently, I did under step and made a .xtc file only for surfactants: i- trjconv -f md.trr -o md-surfactant.xtc -n index.ndx Then I did steps a, b and c for md-surfactant.xtc and in all of steps I selected surfactants for clustering and output group. Next, I did g_clustsize and it answered me correct. May I know that my way is correct, please? 3- By upper way I have 2 micelles that I got index.ndx file for cluster with maximum size by g_clustsize (maxcluster.ndx). May I know how can I use from this for next calculation if I want consider only maximum cluster with all of system (water and ion) in calculations (for example rdf, gyration and etc)? Again I think you are not using the word cluster in the sense the GROMACS tools are. Each micelle could be a cluster of atoms, or the pair of micelles could be a cluster of micelles. How to use the tools will differ according to what you are trying to calculate on what kind of cluster. Anyway, the atom numbers do not change with the configuration of the atoms, so the same index file group identifies the surfactant atoms in each frame. To identify the *time* of the configuration with the largest diameter, something like g_mindist -max might serve. However you may need to resolve your PBC issue first. Mark -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with umbrella sampling and g_wham
Hello Justin, You are a GOD!! Thanks so much!! This is what the histogram looks like now, http://dl.dropbox.com/u/32738905/Histo_good.png I am under and over sampling in many places. I will generate more sample points and increase the umbrella sampling simulation times to 10ns as recommended by you and your tutorial. Thanks again, Eric LeGresley - Original Message - From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, 26 December, 2011 14:48:31 Subject: Re: [gmx-users] Problem with umbrella sampling and g_wham Eric LeGresley wrote: Hello all, For some time now I have been unable to find a solution to my problem. I am attempting to do umbrella sampling on a protein ligand system. To generate the starting configurations, I use the following mdp file: title = Protein-ligand complex MD Simulation define = -DPOSRES_SMD ;keeps from moving ; Run parameters integrator = md; leap-frog integrator nsteps = 25; 2 * 25 fs = 500 ps (0.5 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; suppress .trr output nstvout = 0 ; suppress .trr output nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps nstxtcout = 500 ; write .xtc trajectory every 1 ps energygrps = Protein_CA MOL ; Bond parameters continuation= yes ; first dynamics run 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 = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; 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 ;COM Pulling pull = umbrella pull_geometry = direction pull_start= yes pull_dim = Y Y Y pull_group0 = Protein_CA pull_group1 = MOL pull_vec1 = -2.4 -1.0 -0.4 pull_rate1= 0.008 ; will pull 4nm during the 500ps run pull_k1 = 500 ; Temperature coupling is on tcoupl = nose-hoover tc-grps = Protein_MOL Water_and_ions; two coupling groups - more accurate tau_t = 0.2 0.2 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; 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 = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed A distance vs time graph of this 500ps simulation is here: http://dl.dropbox.com/u/32738905/Dist_SMD500_upped50.png I then run umbrella sampling on 21 of the 500 generated starting configurations to use as input for g_wham. The mdp file I use for the umbrella sampling is as follows: title = MD Run Umbrella define = -DPOSRES_SMD ; protein does not move ; Run parameters integrator = md; leap-frog integrator nsteps = 100 ; 2 * 100 = 2000 ps (2ns) dt = 0.002 ; 2 fs tinit = 0 ; Output control nstxout = 5 ; save coordinates every 10 ps nstvout = 5 ; save velocities every 10 ps nstfout = 5000 ; every 10 ps nstxtcout = 5000 ; every 10 ps nstenergy = 5000 ; save energies every 10 ps nstlog = 5000 ; update log file every 10 ps energygrps = Protein_CA MOL ; Bond parameters continuation= yes ; first dynamics run 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
[gmx-users] Modify charge groups
Dear Justin, Thank you very much for your response. I have another question to continue my calculations. To correct charges and charge groups I have to: 1) seprate the molecule to functional groups 2) some of these functional groups are already exist in selected force field ( in aminoacid.rtp) with their charges, so as you said in fifth tutorial life is pretty easy 3) for new functional groups I have to: i) do QM calculation ii) calculate free energy of solvation or logP iii) compare simulation results with experimental data my questions are when my simulation results do not have any consistence with experimental data, how can I modify new functional groups? and how can I decide which one of atoms have improper charge? Thanks a lot in advance. P.Haghighi -- 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] Compile error : libgmx.so: undefined reference to `pthread_setaffinity_np'
Hello gmx-users -- The following error occurs during compilation of Gromacs 4.5.5 : 4.5.5/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so: undefined reference to `pthread_setaffinity_np' There was an exchange on this problem on the gmx-users list on 21/09/2011, but apparently no solution. OS : RHEL 4 CPU: Dual-Core AMD Opteron Processor 2220 gcc: 3.4.6 20060404 (Red Hat 3.4.6-11) glibc : glibc-2.3.4-2.54 The following is from the configure script : FFTW=/afs/cad/hpc/amd/opt/fftw/3.3/gnu3 INSTALL_DIR=/some/dir CPPFLAGS=-I$FFTW/include LDFLAGS=-L$FFTW/lib time ./configure \ CPPFLAGS=$CPPFLAGS \ LDFLAGS=$LDFLAGS \ --prefix=$INSTALL_DIR \ --with-fft=fftw3 \ 21 | tee -a CONFIGURE.log Any suggestions on how to resolve this problem would be greatly appreciated. Thanks. ___ David Perel IST University Computing Systems (UCS) New Jersey Institute of Technology dav...@njit.edu -- 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] Modify charge groups
parto haghighi wrote: Dear Justin, Thank you very much for your response. I have another question to continue my calculations. To correct charges and charge groups I have to: 1) seprate the molecule to functional groups 2) some of these functional groups are already exist in selected force field ( in aminoacid.rtp) with their charges, so as you said in fifth tutorial life is pretty easy For a single (isolated, non-polymerized) molecule, there is no real need to build .rtp entries. You can just construct an .itp file directly. Either approach would work, I suppose, but there are online tools that write .itp files for you that can be modified. 3) for new functional groups I have to: i) do QM calculation ii) calculate free energy of solvation or logP iii) compare simulation results with experimental data my questions are when my simulation results do not have any consistence with experimental data, how can I modify new functional groups? and how can I decide which one of atoms have improper charge? Such is the difficulty of empirical parameterization. If you're dealing with a small enough model compound, then it is trivial to see which components of the nonbonded energy (van der Waals or Coulombic terms) are too large or too small. You can scale parameters as needed. I have generally found that charges make the biggest difference, but really exotic molecules may require more extensive reparameterization of vdW or bonded terms. -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] Compile error : libgmx.so: undefined reference to `pthread_setaffinity_np'
David Perel wrote: Hello gmx-users -- The following error occurs during compilation of Gromacs 4.5.5 : 4.5.5/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so: undefined reference to `pthread_setaffinity_np' There was an exchange on this problem on the gmx-users list on 21/09/2011, but apparently no solution. OS : RHEL 4 CPU: Dual-Core AMD Opteron Processor 2220 gcc: 3.4.6 20060404 (Red Hat 3.4.6-11) This is a very old GCC. I suspect if you want to use threading, you will need a newer version. Alternatively, you can disable threads during configuration. -Justin glibc : glibc-2.3.4-2.54 The following is from the configure script : FFTW=/afs/cad/hpc/amd/opt/fftw/3.3/gnu3 INSTALL_DIR=/some/dir CPPFLAGS=-I$FFTW/include LDFLAGS=-L$FFTW/lib time ./configure \ CPPFLAGS=$CPPFLAGS \ LDFLAGS=$LDFLAGS \ --prefix=$INSTALL_DIR \ --with-fft=fftw3 \ 21 | tee -a CONFIGURE.log Any suggestions on how to resolve this problem would be greatly appreciated. Thanks. ___ David Perel IST University Computing Systems (UCS) New Jersey Institute of Technology dav...@njit.edu -- 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] Compile error : libgmx.so: undefined reference to `pthread_setaffinity_np'
} From gmx-users-boun...@gromacs.org Tue Dec 27 19:25:23 2011 } Subject: Re: [gmx-users] Compile error : libgmx.so: undefined reference to } `pthread_setaffinity_np' } } David Perel wrote: } Hello gmx-users -- } } The following error occurs during compilation of Gromacs 4.5.5 : } }4.5.5/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so: undefined reference to `pthread_setaffinity_np' } } There was an exchange on this problem on the gmx-users list on 21/09/2011, } but apparently no solution. } } OS : RHEL 4 } } CPU: Dual-Core AMD Opteron Processor 2220 } } gcc: 3.4.6 20060404 (Red Hat 3.4.6-11) } } } This is a very old GCC. I suspect if you want to use threading, you will need a } newer version. Alternatively, you can disable threads during configuration. Thanks. I'll try a GCC 4.1, and also disabling threading in the GCC 3.4.6 build. } } -Justin } } glibc : glibc-2.3.4-2.54 } } The following is from the configure script : } } FFTW=/afs/cad/hpc/amd/opt/fftw/3.3/gnu3 } } INSTALL_DIR=/some/dir } CPPFLAGS=-I$FFTW/include } LDFLAGS=-L$FFTW/lib } } time ./configure \ } CPPFLAGS=$CPPFLAGS \ } LDFLAGS=$LDFLAGS \ } --prefix=$INSTALL_DIR \ } --with-fft=fftw3 \ } 21 | tee -a CONFIGURE.log } } Any suggestions on how to resolve this problem would be greatly appreciated. } } Thanks. } } ___ } David Perel } IST University Computing Systems (UCS) } New Jersey Institute of Technology } dav...@njit.edu } } -- } } } Justin A. Lemkul } Ph.D. Candidate } ICTAS Doctoral Scholar } MILES-IGERT Trainee } Department of Biochemistry } Virginia Tech } Blacksburg, VA } jalemkul[at]vt.edu | (540) 231-9080 } http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin } } } -- } gmx-users mailing listgmx-users@gromacs.org } http://lists.gromacs.org/mailman/listinfo/gmx-users } Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! } Please don't post (un)subscribe requests to the list. Use the } www interface or send it to gmx-users-requ...@gromacs.org. } Can't post? Read http://www.gromacs.org/Support/Mailing_Lists } -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] dodecahedron box
hi dear all users I'm simulating 2 proteins in a dodecahedron unit cell,and I want to put these 2 proteins in an exact distance from each other, and also from the boundaries, and I have some questions for doing this. 1) How can I implement this exact distance from the other protein and also the edges of the box? 2) when I use dodecahedron unit cell with this command: editconf -f protein.gro -o protein_newbox.gro -bt dodecahedron -d 1.0 -c, the first protein is in the center of the box, but as I want to add the second protein at the distance of 1.0 nm from the first one, I decided to determine box vectors and protein position myself, and I wrote: editconf -f protein.gro -o protein_newbox.gro -box 4 4 6 -angles 60 60 90 -center 2 2 2, but a part of protein becomes outside the boundaries. I've examined the other numbers for -box vectors and -center, but the result was the same. I don't know what to do, please help me. thank you in advanced. -zahra -- 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] dodecahedron box
Hi Zahra, You could first create rectangular boxes for each of the two, using -d 0.5 Then translate one over the first box vector length of the other (along x: editconf -translate). Put the two coordinate sets together and generate a rhombic dodecahedron for the combined set. Cheers, Tsjerk On Dec 28, 2011 7:42 AM, Zahra M s_zahra_mous...@yahoo.com wrote: hi dear all users I'm simulating 2 proteins in a dodecahedron unit cell,and I want to put these 2 proteins in an exact distance from each other, and also from the boundaries, and I have some questions for doing this. 1) How can I implement this exact distance from the other protein and also the edges of the box? 2) when I use dodecahedron unit cell with this command: editconf -f protein.gro -o protein_newbox.gro -bt dodecahedron -d 1.0 -c, the first protein is in the center of the box, but as I want to add the second protein at the distance of 1.0 nm from the first one, I decided to determine box vectors and protein position myself, and I wrote: editconf -f protein.gro -o protein_newbox.gro -box 4 4 6 -angles 60 60 90 -center 2 2 2, but a part of protein becomes outside the boundaries. I've examined the other numbers for -box vectors and -center, but the result was the same. I don't know what to do, please help me. thank you in advanced. -zahra -- 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] how to obtain error bar for plotting?
Dear all For what parameters I can use g_analyze -av average.xvg -errbar stddev -f *.xvg? Can I use above tool for obtaining error bars for a *.xvg file resulting from g_dist? I want to obtain a file (containing error bar) to plot with excel. Best Regard -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to obtain error bar for plotting?
On 28/12/2011 6:47 PM, leila karami wrote: Dear all For what parameters I can use g_analyze -av average.xvg -errbar stddev -f *.xvg? Can I use above tool for obtaining error bars for a *.xvg file resulting from g_dist? I want to obtain a file (containing error bar) to plot with excel. What quantity do you wish to show with an error bar? 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] how to obtain error bar for plotting?
Dear Mark thanks for your reply. I have a general questions: For what parameters I can use g_analyze -av average.xvg -errbar stddev -f *.xvg?* What quantity do you wish to show with an error bar? I want to show output from g_dist with an error bar. -- 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
