[gmx-users] Calculating the radius of gyration of clusters
Dear all, I ran MD simulations of a small molecule and clustered structurally similar frames together. I wanted to find the radius of gyration of all the members of each cluster. To do the same, I used the command: $ g_gyrate -f cluster.xtc -s full.tpr -o cluster_rg.xvg Here, the file "cluster.xtc" was obtained as output from the g_cluster command. When I ran the above command, I got the following error multiple times: There were 10 inconsistent shifts. Check your topology. Is there a better way of finding the radius of gyration of all the cluster members in a given cluster? Please suggest how I should go about. Thank you Regards, Gayathri -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] GMX GPU Rest Time
Hello, I recently changed the number of cpus I was pairing with each gpu and I noticed a significant slowdown, more than I would have expected simply due to a reduction in the number of cpus. >From the log file it appears that the GPU is resting for a large amount of time. Is there something I can do about this? I have attached parts of the log file. For reference this is a REMD simulation with 60 replicas on 360 cpus and 60 gpus. I have set the local variable OMP_NUM_THREADS to six in order to assign 6 cpus to each replica and avoid domain decomposition for my small system (as recommend in an earlier correspondence). Any help is appreciated, Dan - GROMACS: gmx mdrun, VERSION 5.1.4 Executable: /home/dkozuch/programs/gromacs_514_gpu/bin/gmx_514_gpu Data prefix: /home/dkozuch/programs/gromacs_514_gpu Command line: gmx_514_gpu mdrun -v -deffnm 1msi_eq -multidir 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 -pin on GROMACS version:VERSION 5.1.4 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support:enabled OpenCL support: disabled invsqrt routine:gmx_software_invsqrt(x) SIMD instructions: AVX2_256 FFT library:fftw-3.3.4-sse2-avx RDTSCP usage: enabled C++11 compilation: disabled TNG support:enabled Tracing support:disabled Built on: Mon May 22 18:29:21 EDT 2017 Built by: dkoz...@tigergpu.princeton.edu [CMAKE] Build OS/arch: Linux 3.10.0-514.16.1.el7.x86_64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz Build CPU family: 6 Model: 79 Stepping: 1 Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc GNU 4.8.5 C compiler flags:-march=core-avx2-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds C++ compiler: /usr/bin/c++ GNU 4.8.5 C++ compiler flags: -march=core-avx2-Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds Boost version: 1.53.0 (external) CUDA compiler: /usr/local/cuda-8.0/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on Sun_Sep__4_22:14:01_CDT_2016;Cuda compilation tools, release 8.0, V8.0.44 CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_60,code=compute_60;-gencode;arch=compute_61,code=compute_61;-use_fast_math;; ;-march=core-avx2;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds; CUDA driver:8.0 CUDA runtime: 8.0 Number of logical cores detected (28) does not match the number reported by OpenMP (6). Consider setting the launch configuration manually! Running on 15 nodes with total 420 cores, 420 logical cores, 24 compatible GPUs Cores per node: 28 Logical cores per node: 28 Compatible GPUs per node: 0 - 4 Different nodes have different type(s) and/or order of GPUs Hardware detected on host tiger-i20g2 (the node of MPI rank 4): CPU info: Vendor: GenuineIntel Brand: Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz Family: 6 model: 79 stepping: 1 CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic SIMD instructions most likely to fit this hardware: AVX2_256 SIMD instructions selected at GROMACS compile time: AVX2_256 GPU info: Number of GPUs detected: 4 #0: NVIDIA Tesla P100-PCIE-16GB, compute cap.: 6.0, ECC: yes, stat: compatible #1: NVIDIA Tesla P100-PCIE-16GB, compute cap.: 6.0, ECC: yes, stat: compatible #2: NVIDIA Tesla P100-PCIE-16GB, compute cap.: 6.0, ECC: yes, stat: compatible #3: NVIDIA Tesla P100-PCIE-16GB, compute cap.: 6.0, ECC: yes, stat: compatible This is simulation 4 out of 60 running as a composite GROMACS multi-simulation job. Setup for this simulation: Using 1 MPI process Using 6 OpenMP threads 4 compatible
[gmx-users] Enquiry about simulating the aggregation behavior of bile salts in GROMACS
Dear users, I am planing to simulate how small organic molecules (i.e. pyrene and phenanthrene) bind to bile salts in the gut using GROMACS. However, there are diverse groups of bile salts in the intestinal systems. Could someone give me some suggestion on choosing one typical type of bile salts for the study? Which force field is better? Many thanks for your time and help! Sincerely yours, Xujun Liang -- Xujun LIANG, PhD School of Environment and Energy South China University of Technology Guangzhou, 510006 Guangdong Province China Best wishes to you!! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] number of coordinates does not match after POSRES
Hi Justin, Thanks for your advice. Since we are using a forcefield which could only incorporate with gromacs 3.3.1, we have no choice but to prepare the system in the old version, then run it with the latest version of gromacs. Yes, indeed the option should be with -DPOSRES instead. And the topology file should #include chainA-pace.top, then chainA_posres.itp in this alternative manner. It seems that writing all chainA chainB.top first and all pores.itp later would not do it. Please tell me if I am wrong. Simon 2017-06-07 19:57 GMT+08:00 Justin Lemkul : > > > On 6/7/17 7:18 AM, Simon Kit Sang Chu wrote: > >> Hi Mark, >> >> Thanks for your prompt reply. What surprises me is that a change of >> "define >> = POSRES" could cause a problem. The full output from grompp is - >> >> checking input for internal consistency... >> calling cpp... >> cpp: error: POSRES: No such file or directory >> > > Well, here's the first problem. Your syntax is incorrect (#ifdef keywords > are prefixed with -D, so "define = POSRES" does nothing but "define = > -DPOSRES" would invoke position restraints. > > cpp: warning: ‘-x c’ after last input file has no effect >> cpp: fatal error: no input files >> compilation terminated. >> cpp exit code: 1024 >> Tried to execute: 'cpp -I/home/simon/Softs/gromacs-3. >> 3.1/share/gromacs/top >> POSRES p1p2.top > gromppDTyNuM' >> The 'cpp' command is defined in the .mdp file >> processing topology... >> processing coordinates... >> --- >> Program grompp, VERSION 3.3.1 >> > > Is there a reason you are using prehistoric, deprecated software? > > Source code file: grompp.c, line: 448 >> >> Fatal error: >> number of coordinates in coordinate file (npt.gro, 74787) >> does not match topology (p1p2.top, 0) >> >> > This suggests mangled syntax, so check for typos, bad line endings, etc. > and use a more modern GROMACS version. > > -Justin > > >> The additional information is attached here as a reference. >> >> *chainA-pace.top* >> [ moleculetype ] >> ; Namenrexcl >> Protein_A 3 >> >> [ atoms ] >> ; nr type resnr residue atom cgnr charge mass typeB >> chargeB massB >> 1 N+ 1MET N 10.7 17 ; >> qtot 0.7 >> . >> . >> . >>919 922 921 920 20.0 300.0 >> >> ; Include Position restraint file >> #ifdef POSRES >> #include "chainA_posre.itp" >> #endif >> >> >> *chainA_porse.itp* >> >> ; position restraints for r_1-62_&_Backbone of FullP1P2 in water >> >> [ position_restraints ] >> ; i funct fcxfcyfcz >> 11 1000 1000 1000 >> . >> . >> . >> 5231 1000 1000 1000 >> 5301 1000 1000 1000 >> >> Simon >> >> >> 2017-06-07 16:28 GMT+08:00 Mark Abraham : >> >> Hi, >>> >>> We can't tell, because position restraints are an attribute of >>> moleculetypes and those are hidden in your itp files and you didn't share >>> which moleculetype grompp reported was the problem. Please copy and paste >>> terminal output to make a useful description. >>> >>> You'll need to include the position restraint file appropriate to each >>> moleculetype, of course - not the same one each time. >>> >>> Mark >>> >>> On Wed, 7 Jun 2017 08:58 Simon Kit Sang Chu >>> wrote: >>> >>> Hi, Initially, my topology file can run grompp with .mdp and .gro. However, after putting POSRES in my mdp, the warning "number of coordinates does >>> not >>> match" and there is no coordinate recognized in my topology file anymore. Therefore, the option POSRES somehow changes everything. The topology file is put here. Is there anything I have written incorrectly? ; Include forcefield parameters #include "ffPACE_1.3.itp" ; Include chain topologies #include "chainA-pace.top" #include "chainB-pace.top" ; Include water topology #include "cgWater.itp" ; Include topology for ions #include "martini_v2.0_ions.itp" [ system ] ; Name FullP1P2 in water [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1` SOL 72899 NA+ 20 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/Support >>> /Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests
[gmx-users] summary_distances.dat file not complete
Dear users, I ran the Perl script for Umbrella Sampling Tutorial 3, and it generated an incomplete summary_distances.dat : summary_distances.dat : 00.505 10.507 20.504 30.510 40.505 50.500 60.499 70.509 80.505 90.504 100.510 110.505 120.509 130.508 140.511 150.513 160.504 170.499 180.512 190.504 200.506 210.510 220.504 230.498 240.496 250.507 260.504 270.501 280.509 290.512 300.508 310.511 320.501 330.508 340.503 350.507 360.511 370.503 380.506 390.503 400.512 410.502 420.503 430.503 440.503 450.500 460.492 470.507 480.503 490.501 500.501 510.501 520.504 530.500 540.504 550.507 560.504 570.514 580.506 590.509 600.504 610.503 620.505 630.502 640.508 650.496 660.499 670.507 680.507 690.512 700.500 710.507 720.498 730.500 740.499 750.509 760.507 770.504 780.506 790.502 800.510 810.507 820.513 830.504 840.516 850.509 860.504 870.510 880.504 890.509 900.515 910.513 920.516 930.513 940.514 950.519 960.507 970.521 980.505 990.514 1000.508 1010.510 1020.520 1030.514 1040.507 1050.512 1060.506 1070.510 1080.508 1090.506 1100.512 1110.519 1120.519 1130.521 1140.506 1150.508 1160.518 1170.521 1180.520 1190.519 1200.507 1210.515 1220.523 1230.529 1240.525 1250.528 1260.516 1270.536 1280.538 1290.533 1300.538 1310.540 1320.543 1330.551 1340.550 1350.552 1360.552 1370.549 1380.541 1390.542 1400.550 1410.563 1420.551 1430.553 1440.554 1450.541 1460.551 1470.557 1480.558 1490.557 1500.562 1510.566 1520.553 1530.566 1540.568 1550.570 1560.579 1570.594 1580.580 1590.582 1600.579 1610.583 1620.580 1630.604 1640.631 1650.632 1660.629 1670.631 1680.625 1690.626 1700.642 1710.633 1720.649 1730.645 1740.644 1750.640 1760.648 1770.669 1780.668 1790.673 1800.687 1810.697 1820.698 1830.711 1840.725 1850.739 1860.732 1870.735 1880.744 1890.753 1900.798 1910.813 1920.820 1930.845 1940.847 1950.883 1960.903 1970.908 1980.926 1990.984 2001.024 2011.056 2021.110 2031.174 2041.247 2051.295 2061.320 2071.388 2081.410 2091.452 2101.509 2111.550 2121.592 2131.600 2141.675 2151.728 2161.824 2171.867 2181.934 2191.958 2201.990 2212.060 2222.083 2232.137 2242.199 2252.242 2262.260 2272.297 2282.349 2292.375 2302.406 2312.410 2322.454 2332.505 2342.499 2352.535 2362.572 2372.579 2382.570 2392.619 2402.609 2412.646 2422.654 2432.666 2442.696 2452.725 2462.728 2472.733 2482.737 2492.763 2502.760 2512.760 2522.783 2532.793 2542.821 2552.847 2562.864 2572.873 2582.900 2592.924 2602.937 2612.971 2623.012 2633.029 2643.031 2653.004 2663.018 2673.047 2683.034 2693.026 2703.055 2713.043 2723.058 2733.103 2743.111 2753.116 2763.114 2773.112 2783.124 2793.130 2803.151 2813.166 2823.154 2833.182 2843.174 2853.194 2863.199 2873.184 2883.228 2893.260 2903.263 2913.298 2923.305 2933.319 2943.331 2953.343 2963.357 2973.367 2983.381 2993.374 3003.398 3013.409 3023.430 3033.465 3043.504 3053.491 3063.506 3073.514 3083.513 3093.526 3103.529 3113.512 3123.512 3133.534 3143.553 3153.582 3163.584 3173.561 3183.585 3193.596 3203.614 3213.618 3223.616 3233.607 3243.603 3253.624 3263.658 3273.674 3283.660 3293.665 3303.652 3313.683 3323.699 3333.714 3343.771 3353.798 3363.815 3373.818 3383.830 3393.833 3403.837 3413.812 3423.808 3433.823 3443.819 3453.856 3463.881 3473.890 3483.923 3493.948 3503.980 3513.979 3523.938 3533.940 3543.943 3553.954 3563.976 3573.972 3583.950 3593.955 3603.959 3613.988 3623.993 3634.012 3644.032 3654.039 3664.062 3674.050 3684.048 3694.064 3704.072 3714.071 3724.095 3734.102 3744.089 3754.096 3764.069 3774.081 3784.062 3794.081 3804.120 381
[gmx-users] Technqiues for Applying Assymmetric Ion Concentrations?
Hello Users, I am planning to do a bilayer simulation with asymmetric ion concentrations using slab boundaries. I am trying to modify the concentration of each ionic species on each side of the bilayer, however, I am struggling to find a technique that will allow me to effectively manipulate the concentrations of each side of the bilayer. Are there any suggestions on how to do this? I would imagine splitting the system in half at the hydrophobic core and then using the genion command for each half would do the trick but I am unaware of any commands that will allow me to split the system as such. The membrane system that I am using is from CHARMM-GUI. I will truly appreciate your input. Regards, Sanim Rahman -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Remove all but N closest water molecules from protein
Dear Gromacs users, I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow me to create a new *.gro file containing the protein and the N closest water molecules to the protein , starting from a system of a solvated protein ? Best, Jose Borreguero -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx insert-molecules
> 在 2017年6月7日,16:26,gromacs.org_gmx-users-requ...@maillist.sys.kth.se 写道: > > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Cylinder pulling through bilayer (Gmx QA) > 2. Re: gmx insert-molecules (Justin Lemkul) > 3. deltaG shifts in g_wham (Alex) > 4. Re: deltaG shifts in g_wham (Justin Lemkul) > 5. problem with "gmx rdf": It cannot find the center of mass of > a reference group (Sajjad Kavyani) > 6. problem with "gmx rdf": It cannot find the center of mass of > a reference group (Sajjad Kavyani) > > > -- > > Message: 1 > Date: Wed, 7 Jun 2017 21:22:04 +0200 > From: Gmx QA > To: Discussion list for GROMACS users > Subject: [gmx-users] Cylinder pulling through bilayer > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Dear list > > I am attempting to pull a small molecule though a bilayer using the pull > geometry cylinder with gromacs v 2016. > > This is the relevant portion of my mdp-file: > > pull = yes > pull-ngroups = 2 > pull-ncoords = 1 > pull-coord1-groups = 1 2 > pull-group1-name = LIG > pull-group2-name = MEM > pull-coord1-type = umbrella > pull-coord1-geometry = cylinder > pull-coord1-rate = 0.1 > pull-coord1-vec = 0 0 1 > pull-coord1-k= 1000 > pull-coord1-start= yes > pull-coord1-init = 0 > pull-cylinder-r = 1.5 > > The pull-rate is very fast because I'm only doing preliminary test. At the > start, the drug molecule is in -z position compared to the membrane. > > When doing grompp: > > $ gmx grompp -f umbrella_md_test.mdp -c npt.gro -p topol.top -o > pull_test.tpr > > The output makes no sense: > Using a fourier grid of 72x72x192, spacing 0.113 0.113 0.111 > Pull group natoms pbc atom distance at start reference at t=0 > 13618 > 2 32500 64286-nan nm -nan nm > Estimate for the relative computational load of the PME mesh part: 0.44 > This run will generate roughly 14 Mb of data > > > I.e. nan's for distance. If I however switch in the mdp file so that > pull-group1-name = MEM and pull-group2-name = LIG, the distance gets > correctly calculated. But this does not seem to be what is prescribed in > the manual for cylinder pulling, where is says that the cylinder is formed > from the first group (should be the drug molecule) and through the com of > the reference group (the membrane in my case), > > I think there is something I am missing? > > Thanks! > /PK > > > -- > > Message: 2 > Date: Wed, 7 Jun 2017 16:07:54 -0400 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] gmx insert-molecules > Message-ID: <72ae4ffd-7c78-05ec-fb7f-5784e8e6b...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > Please do not reply to the whole digest. > > On 6/7/17 2:46 PM, Shi Li wrote: >>> >>> On 6/7/17 1:20 PM, Li, Shi wrote: Dear GMX users, I have a pure solvent system A with 100 molecules. Then I randomly removed 10 molecules out of the box, but keep the box size. Now I want to do a gmx insert-molecule to insert 10 molecule B into the system box. The problem is molecule B is slightly larger than molecule A. So in some cases, I couldn't insert the exact 10 molecules of B into the system. Is there a way to automatically adjust the size of the box according to the radius of molecule B, so that they can fit in? Or, is there a better solution to do this? >>> >>> Insert 10 of molecule B into an empty box, then solvate with a >>> pre-equilibrated >>> box of molecule A. Works every time. >>> >>> -Justin >> >> Thank you Justin, >> >> In this case, I will need to apply a full equilibrium process (em, nvt, npt) >> to the new system, is that right? >> >> I am trying to avoid the long step of equilibrium as I have many systems >> corresponding to different concentrations. I was thinking if I replace a >> small number of molecule A with molecule B (the system A is very large and >> pre-equilibriumed) then I only need to apply a short time-step of NPT in >> order to let the system expand or shrink. Then I can use the new system to >> continue replacing A with B to generate a new concentratio
Re: [gmx-users] problem with "gmx rdf": It cannot find the center of mass of a reference group
Finally I managed to find the exact syntax for the rdf calculation by adding " -ref 'com of group g1' " at the end of the command-line: gmx rdf -f cgs.gro -s cgs.tpr -o rdf.xvg -xy -ref 'com of group g1' On Thu, Jun 8, 2017 at 12:56 AM, Sajjad Kavyani wrote: > Dear experts, > Recently I ask a question entitled "RDF of a group around CNT axis" in > the mailing list in order to find proper command-line for it it turns out > that the "-xy" option can help > But I encounter an unusual problem therefore I decided to ask another > question > > It turns out that the gmx rdf cannot find the com coordinate of the CNT > (as reference) because as I choose different command-lines with various > "-selrpos" arguments, all of the results gave me EXACTLY the SAME result > which all of them are wrong! Commands like: > gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg > gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg -selrpos res_com > gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg -selrpos res_cog > gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg -selrpos mol_com > gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg -selrpos mol_cog > (CNT group has been chosen for both groups is gmx rdf) > > But when I manually placed a single particle in the COM of the cnt (in the > cgs.gro) and then select this single particle as reference group, the gmx > rdf resulted the desired value! > > > Could you please help me to manage the problem? > How to tell the gmx rdf in order to find com of cnt without manually > placing a single particle in the input file? > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] problem with "gmx rdf": It cannot find the center of mass of a reference group
Dear experts, Recently I ask a question entitled "RDF of a group around CNT axis" in the mailing list in order to find proper command-line for it it turns out that the "-xy" option can help But I encounter an unusual problem therefore I decided to ask another question It turns out that the gmx rdf cannot find the com coordinate of the CNT (as reference) because as I choose different command-lines with various "-selrpos" arguments, all of the results gave me EXACTLY the SAME result which all of them are wrong! Commands like: gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg -selrpos res_com gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg -selrpos res_cog gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg -selrpos mol_com gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg -selrpos mol_cog (CNT group has been chosen for both groups is gmx rdf) But when I manually placed a single particle in the COM of the cnt (in the cgs.gro) and then select this single particle as reference group, the gmx rdf resulted the desired value! Could you please help me to manage the problem? How to tell the gmx rdf in order to find com of cnt without manually placing a single particle in the input file? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] deltaG shifts in g_wham
On 6/7/17 4:18 PM, Alex wrote: Hi all, I am using 'gmx wham' (GMX 5.0.4) on a system that consists of a membrane with a narrow pore and an ion. The configurations correspond to various heights "above" the membrane (0 to 1.5 nm). In one case, the ion is K+, in another Na+. In both cases the results are fairly reasonable, but there is a bit of a numerical caveat. For sodium, the free energy away from the pore is close to zero and considerably negative inside the pore, as one might expect. For potassium (the input files are nearly identical), the free energy far away from the pore is a considerable _positive_ value and zero inside the pore. I do realize that absolute values are meaningless and I can always "shift" the results to correspond to near-zero far away from the reactive site (and when I do, I even have reasonable agreement with experiment). However, I want to understand what is happening with the utility. My simulation times are quite moderate (1 ns for each config). Can someone help? WHAM sets the "left-most" window (i.e. smallest value of zeta) to zero and calculates all free energy values relative to that. This is why you can offset at any given point. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] deltaG shifts in g_wham
Hi all, I am using 'gmx wham' (GMX 5.0.4) on a system that consists of a membrane with a narrow pore and an ion. The configurations correspond to various heights "above" the membrane (0 to 1.5 nm). In one case, the ion is K+, in another Na+. In both cases the results are fairly reasonable, but there is a bit of a numerical caveat. For sodium, the free energy away from the pore is close to zero and considerably negative inside the pore, as one might expect. For potassium (the input files are nearly identical), the free energy far away from the pore is a considerable _positive_ value and zero inside the pore. I do realize that absolute values are meaningless and I can always "shift" the results to correspond to near-zero far away from the reactive site (and when I do, I even have reasonable agreement with experiment). However, I want to understand what is happening with the utility. My simulation times are quite moderate (1 ns for each config). Can someone help? Thanks, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx insert-molecules
Please do not reply to the whole digest. On 6/7/17 2:46 PM, Shi Li wrote: On 6/7/17 1:20 PM, Li, Shi wrote: Dear GMX users, I have a pure solvent system A with 100 molecules. Then I randomly removed 10 molecules out of the box, but keep the box size. Now I want to do a gmx insert-molecule to insert 10 molecule B into the system box. The problem is molecule B is slightly larger than molecule A. So in some cases, I couldn't insert the exact 10 molecules of B into the system. Is there a way to automatically adjust the size of the box according to the radius of molecule B, so that they can fit in? Or, is there a better solution to do this? Insert 10 of molecule B into an empty box, then solvate with a pre-equilibrated box of molecule A. Works every time. -Justin Thank you Justin, In this case, I will need to apply a full equilibrium process (em, nvt, npt) to the new system, is that right? I am trying to avoid the long step of equilibrium as I have many systems corresponding to different concentrations. I was thinking if I replace a small number of molecule A with molecule B (the system A is very large and pre-equilibriumed) then I only need to apply a short time-step of NPT in order to let the system expand or shrink. Then I can use the new system to continue replacing A with B to generate a new concentration. Is this practical? The problem is when B is slightly larger than A, I can’t insert the same number of B into the system. Is there way to avoid the overlapping or force the molecule in? You can reduce the vdW radius of atoms to *try* to force the molecules to fit, but then all you've done is introduce bad clashes that have to be subjected to minimization and re-equilibration. So at that point, all you've done is build your system in the most inefficient way possible. By trying to avoid equilibration, you've necessitated it :) Build the system the robust way - solute first, then solvent. It's ultimately less work and less prone to failure. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Cylinder pulling through bilayer
Dear list I am attempting to pull a small molecule though a bilayer using the pull geometry cylinder with gromacs v 2016. This is the relevant portion of my mdp-file: pull = yes pull-ngroups = 2 pull-ncoords = 1 pull-coord1-groups = 1 2 pull-group1-name = LIG pull-group2-name = MEM pull-coord1-type = umbrella pull-coord1-geometry = cylinder pull-coord1-rate = 0.1 pull-coord1-vec = 0 0 1 pull-coord1-k= 1000 pull-coord1-start= yes pull-coord1-init = 0 pull-cylinder-r = 1.5 The pull-rate is very fast because I'm only doing preliminary test. At the start, the drug molecule is in -z position compared to the membrane. When doing grompp: $ gmx grompp -f umbrella_md_test.mdp -c npt.gro -p topol.top -o pull_test.tpr The output makes no sense: Using a fourier grid of 72x72x192, spacing 0.113 0.113 0.111 Pull group natoms pbc atom distance at start reference at t=0 13618 2 32500 64286-nan nm -nan nm Estimate for the relative computational load of the PME mesh part: 0.44 This run will generate roughly 14 Mb of data I.e. nan's for distance. If I however switch in the mdp file so that pull-group1-name = MEM and pull-group2-name = LIG, the distance gets correctly calculated. But this does not seem to be what is prescribed in the manual for cylinder pulling, where is says that the cylinder is formed from the first group (should be the drug molecule) and through the com of the reference group (the membrane in my case), I think there is something I am missing? Thanks! /PK -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx insert-molecules
> 在 2017年6月7日,13:31,gromacs.org_gmx-users-requ...@maillist.sys.kth.se 写道: > > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: Simulate protein at subzero condition in aqueous buffer > (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=) > 2. Re: Simulate protein at subzero condition in aqueous buffer > (Jo?o Henriques) > 3. gmx insert-molecules (Li, Shi) > 4. Re: gmx insert-molecules (Justin Lemkul) > 5. Re: Simulate protein at subzero condition in aqueous buffer > (Jo?o Henriques) > > > -- > > Message: 1 > Date: Thu, 8 Jun 2017 01:07:40 +0800 > From: "=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=" <272699...@qq.com> > To: "=?ISO-8859-1?B?Z3JvbWFjcy5vcmdfZ214LXVzZXJz?=" > > Subject: Re: [gmx-users] Simulate protein at subzero condition in > aqueous buffer > Message-ID: > Content-Type: text/plain; charset="ISO-8859-1" > > Dear Justin, > Thank you very much. I will try the possible water models. > > > Do you know if there are water models to resemble frozen state? > > > Yours sincerely > Cheng > > > > > -- Original -- > From: "ZHANG Cheng";<272699...@qq.com>; > Date: Thu, Jun 8, 2017 00:50 AM > To: "ZHANG Cheng"<272699...@qq.com>; > "gromacs.org_gmx-users"; > > Subject: Re: Simulate protein at subzero condition in aqueous buffer > > > > Dear Joao, > Thank you for your help and the paper link. > > > I was following Justin's tutorial > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html > On that page, it says "spc216.gro as the solvent configuration for SPC, > SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) > after the solvation step. So I assume "spc216.gro" refer to all the > three-point water models? > > > I am trying to see if my protein will be denatured in cold condition. > > > Yours sincerely > Cheng > > > -- Original -- > From: "ZHANG Cheng";<272699...@qq.com>; > Date: Wed, Jun 7, 2017 10:01 PM > To: "gromacs.org_gmx-users"; > Cc: "ZHANG Cheng"<272699...@qq.com>; > Subject: Simulate protein at subzero condition in aqueous buffer > > > > Dear Gromacs, > I would like to simulate the protein at subzero condition in aqueous buffer, > to see if it becomes more stable than the elevated temperature (e.g. 65 C). > Can I ask what is the valid temperature range for water "spc216.gro" ? If I > run the simulation at -40 C, does it still assume the system as liquid state > instead of frozen state? Thank you. > > > Yours sincerely > Cheng > > -- > > Message: 2 > Date: Wed, 7 Jun 2017 19:15:58 +0200 > From: Jo?o Henriques > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Simulate protein at subzero condition in > aqueous buffer > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > ?Higher complexity water models such as TIP5P and so on are able to better > reproduce bulk water properties (please check the paper I linked in my > earlier email). However, these models require more computational effort > (due to the increased number of interactions) and may not work well in > conjunction with a protein (many protein force fields were developed to be > used with specific water models)?. As Justin said, none of them gets > everything right. > > /J > > On Wed, Jun 7, 2017 at 7:07 PM, ZHANG Cheng <272699...@qq.com> wrote: > >> Dear Justin, >> Thank you very much. I will try the possible water models. >> >> >> Do you know if there are water models to resemble frozen state? >> >> >> Yours sincerely >> Cheng >> >> >> >> >> -- Original -- >> From: "ZHANG Cheng";<272699...@qq.com>; >> Date: Thu, Jun 8, 2017 00:50 AM >> To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"> s.org_gmx-us...@maillist.sys.kth.se>; >> >> Subject: Re: Simulate protein at subzero condition in aqueous buffer >> >> >> >> Dear Joao, >> Thank you for your help and the paper link. >> >> >> I was following Justin's tutorial >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ >> gmx-tutorials/lysozyme/03_solvate.html >> On that page, it says "spc216.gro as the solvent configuration for SPC, >> SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) >> after t
Re: [gmx-users] RDF of a group around CNT axis
I noticed that the gmx rdf some how cannot find the center of mass (COM) for the CNT because after that I manually put a single particle in the COM of the CNT and calculated the rdf around it (with -xy option), the gmx rdf resulted the expected value which is a sharp peak at the radius of the cnt. I tested all the -selrpos arguments but none of them could find the COM of the CNT Could you please help me to manage the problem ? Regards Sajjad On Wed, Jun 7, 2017 at 7:19 PM, Sajjad Kavyani wrote: > Dear Srinivas, > That's absolutely right, I want to calculate the RDF of a certain > group around the central axis of a nanotube. > And as I know that the RDF of the CNT around its axis is just a sharp peak > at the radius, I just tested the command-line parameters for this case, to > specify that which command-line should be used. > > And honestly I do not understand the last sentence of your reply, could > you please specify that after isolating the desired group, what > command-line I should use? > > Sincerely, > Sajjad > > > > On Wed, Jun 7, 2017 at 6:54 PM, SRINIVAS MUSHNOORI < > scm...@scarletmail.rutgers.edu> wrote: > >> If I understand you correctly: you want to calculate the RDF of a certain >> group (NOT part of the nanotube) around the central axis of a nanotube? >> >> The way I do these calculations is to use the gmx trjconv tool to isolate >> a >> trajectory file of ONLY the gropus I am interested in and run my >> calculations on that. >> If you expect to see one peak but see many that might mean that the RDF is >> picking up groups that you don't want it to. >> >> Hope that helps, >> Srinivas >> >> On Wed, Jun 7, 2017 at 9:41 AM, Sajjad Kavyani >> wrote: >> >> > Dear experts, >> > I want to calculate rdf of a certain group around the axis of a cnt, >> but I >> > do not know what are the proper parameters to choose in the >> command-line. >> > To test the parameters, I calculated the rdf of cnt itself around its >> axis >> > which must be a sharp peak at the cnt radius. >> > I tested the following: (both selection groups of reference and rdf are >> > CNT) >> > gmx rdf -f md.gro -s md.tpr -o trdf.xvg -xy -selrpos mol_com >> > gmx rdf -f md.gro -s md.tpr -o trdf.xvg -xy -selrpos res_com >> > gmx rdf -f md.gro -s md.tpr -o trdf.xvg -xy -selrpos whole_res_com >> > gmx rdf -f md.gro -s md.tpr -o trdf.xvg -xy -selrpos whole_mol_com >> > >> > BUT all the results are the same!!! and surprisingly they have multiple >> > sharp peaks at different ranges, which I expected just one peak at the >> > radius of the CNT >> > It is notable that the CNT is aligned to z axis. >> > (the first two peaks are listed below): >> > >> > 0.000 211939.438 >> > 0.002 53771.996 >> > 0.004 11278.401 >> > 0.006 3935.633 >> > 0.008 1782.280 >> > 0.010 809.616 >> > 0.012 584.723 >> > 0.014 536.531 >> > 0.016 292.361 >> > 0.018 149.929 >> > 0.020 94.455 >> > 0.022 00.000 >> > ... >> > ... >> > ... >> > 0.11800.000 >> > 0.1200.375 >> > 0.1222.212 >> > 0.1240.725 >> > 0.1266.069 >> > 0.128 36.545 >> > 0.130 114.868 >> > 0.132 278.390 >> > 0.134 1669.916 >> > 0.136 2360.069 >> > 0.138 346.139 >> > 0.140 183.770 >> > 0.142 39.277 >> > >> > Could you please explain to me that what should I do? >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at http://www.gromacs.org/ >> > Support/Mailing_Lists/GMX-Users_List before posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-requ...@gromacs.org. >> > >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support >> /Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer
Dear Joao, Thank you very much for your support. I am following Justin's tutorial but simulating a fragment of antibody (Fab). I will try the different water models. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, Jun 8, 2017 01:07 AM To: "gromacs.org_gmx-users"; Subject: Re: Re: Simulate protein at subzero condition in aqueous buffer Dear Justin, Thank you very much. I will try the possible water models. Do you know if there are water models to resemble frozen state? Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, Jun 8, 2017 00:50 AM To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"; Subject: Re: Simulate protein at subzero condition in aqueous buffer Dear Joao, Thank you for your help and the paper link. I was following Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) after the solvation step. So I assume "spc216.gro" refer to all the three-point water models? I am trying to see if my protein will be denatured in cold condition. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, Jun 7, 2017 10:01 PM To: "gromacs.org_gmx-users"; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Simulate protein at subzero condition in aqueous buffer Dear Gromacs, I would like to simulate the protein at subzero condition in aqueous buffer, to see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I ask what is the valid temperature range for water "spc216.gro" ? If I run the simulation at -40 C, does it still assume the system as liquid state instead of frozen state? Thank you. Yours sincerely Cheng -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer
Just one more thing. If you're following Justin's tutorial, I guess you're using lysozyme. This protein will not deviate very much from it's crystal structure at 27ºC, let alone at -40ºC (*in the context of a molecular dynamics simulation**). I understand that it may be possible to experimentally unfold this protein reversibly using low temperature and high pressure, but this may be unfeasible to perform using a regular protein force field and water model. It will not behave as you expect. * I should add that this is a very stable protein and the disulfide bonds (which cannot be broken during the simulation) make it almost impossible to unfold it completely at any temperature using molecular dynamics. /J On Wed, Jun 7, 2017 at 7:15 PM, João Henriques wrote: > Higher complexity water models such as TIP5P and so on are able to better > reproduce bulk water properties (please check the paper I linked in my > earlier email). However, these models require more computational effort > (due to the increased number of interactions) and may not work well in > conjunction with a protein (many protein force fields were developed to be > used with specific water models). As Justin said, none of them gets > everything right. > > /J > > On Wed, Jun 7, 2017 at 7:07 PM, ZHANG Cheng <272699...@qq.com> wrote: > >> Dear Justin, >> Thank you very much. I will try the possible water models. >> >> >> Do you know if there are water models to resemble frozen state? >> >> >> Yours sincerely >> Cheng >> >> >> >> >> -- Original -- >> From: "ZHANG Cheng";<272699...@qq.com>; >> Date: Thu, Jun 8, 2017 00:50 AM >> To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"> s.org_gmx-us...@maillist.sys.kth.se>; >> >> Subject: Re: Simulate protein at subzero condition in aqueous buffer >> >> >> >> Dear Joao, >> Thank you for your help and the paper link. >> >> >> I was following Justin's tutorial >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx >> -tutorials/lysozyme/03_solvate.html >> On that page, it says "spc216.gro as the solvent configuration for SPC, >> SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) >> after the solvation step. So I assume "spc216.gro" refer to all the >> three-point water models? >> >> >> I am trying to see if my protein will be denatured in cold condition. >> >> >> Yours sincerely >> Cheng >> >> >> -- Original -- >> From: "ZHANG Cheng";<272699...@qq.com>; >> Date: Wed, Jun 7, 2017 10:01 PM >> To: "gromacs.org_gmx-users"; >> Cc: "ZHANG Cheng"<272699...@qq.com>; >> Subject: Simulate protein at subzero condition in aqueous buffer >> >> >> >> Dear Gromacs, >> I would like to simulate the protein at subzero condition in aqueous >> buffer, to see if it becomes more stable than the elevated temperature >> (e.g. 65 C). Can I ask what is the valid temperature range for water >> "spc216.gro" ? If I run the simulation at -40 C, does it still assume the >> system as liquid state instead of frozen state? Thank you. >> >> >> Yours sincerely >> Cheng >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support >> /Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx insert-molecules
On 6/7/17 1:20 PM, Li, Shi wrote: Dear GMX users, I have a pure solvent system A with 100 molecules. Then I randomly removed 10 molecules out of the box, but keep the box size. Now I want to do a gmx insert-molecule to insert 10 molecule B into the system box. The problem is molecule B is slightly larger than molecule A. So in some cases, I couldn't insert the exact 10 molecules of B into the system. Is there a way to automatically adjust the size of the box according to the radius of molecule B, so that they can fit in? Or, is there a better solution to do this? Insert 10 of molecule B into an empty box, then solvate with a pre-equilibrated box of molecule A. Works every time. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gmx insert-molecules
Dear GMX users, I have a pure solvent system A with 100 molecules. Then I randomly removed 10 molecules out of the box, but keep the box size. Now I want to do a gmx insert-molecule to insert 10 molecule B into the system box. The problem is molecule B is slightly larger than molecule A. So in some cases, I couldn't insert the exact 10 molecules of B into the system. Is there a way to automatically adjust the size of the box according to the radius of molecule B, so that they can fit in? Or, is there a better solution to do this? Or, is there a way to ignore the overlapping of molecules? In that case, even the inserted molecule is overlapping with surrounding molecules, it can still be inserted in? Many thanks, Shi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer
Higher complexity water models such as TIP5P and so on are able to better reproduce bulk water properties (please check the paper I linked in my earlier email). However, these models require more computational effort (due to the increased number of interactions) and may not work well in conjunction with a protein (many protein force fields were developed to be used with specific water models). As Justin said, none of them gets everything right. /J On Wed, Jun 7, 2017 at 7:07 PM, ZHANG Cheng <272699...@qq.com> wrote: > Dear Justin, > Thank you very much. I will try the possible water models. > > > Do you know if there are water models to resemble frozen state? > > > Yours sincerely > Cheng > > > > > -- Original -- > From: "ZHANG Cheng";<272699...@qq.com>; > Date: Thu, Jun 8, 2017 00:50 AM > To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users" s.org_gmx-us...@maillist.sys.kth.se>; > > Subject: Re: Simulate protein at subzero condition in aqueous buffer > > > > Dear Joao, > Thank you for your help and the paper link. > > > I was following Justin's tutorial > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > gmx-tutorials/lysozyme/03_solvate.html > On that page, it says "spc216.gro as the solvent configuration for SPC, > SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) > after the solvation step. So I assume "spc216.gro" refer to all the > three-point water models? > > > I am trying to see if my protein will be denatured in cold condition. > > > Yours sincerely > Cheng > > > -- Original -- > From: "ZHANG Cheng";<272699...@qq.com>; > Date: Wed, Jun 7, 2017 10:01 PM > To: "gromacs.org_gmx-users"; > Cc: "ZHANG Cheng"<272699...@qq.com>; > Subject: Simulate protein at subzero condition in aqueous buffer > > > > Dear Gromacs, > I would like to simulate the protein at subzero condition in aqueous > buffer, to see if it becomes more stable than the elevated temperature > (e.g. 65 C). Can I ask what is the valid temperature range for water > "spc216.gro" ? If I run the simulation at -40 C, does it still assume the > system as liquid state instead of frozen state? Thank you. > > > Yours sincerely > Cheng > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer
Dear Justin, Thank you very much. I will try the possible water models. Do you know if there are water models to resemble frozen state? Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, Jun 8, 2017 00:50 AM To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"; Subject: Re: Simulate protein at subzero condition in aqueous buffer Dear Joao, Thank you for your help and the paper link. I was following Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) after the solvation step. So I assume "spc216.gro" refer to all the three-point water models? I am trying to see if my protein will be denatured in cold condition. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, Jun 7, 2017 10:01 PM To: "gromacs.org_gmx-users"; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Simulate protein at subzero condition in aqueous buffer Dear Gromacs, I would like to simulate the protein at subzero condition in aqueous buffer, to see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I ask what is the valid temperature range for water "spc216.gro" ? If I run the simulation at -40 C, does it still assume the system as liquid state instead of frozen state? Thank you. Yours sincerely Cheng -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer
On 6/7/17 12:50 PM, ZHANG Cheng wrote: Dear Joao, Thank you for your help and the paper link. I was following Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) after the solvation step. So I assume "spc216.gro" refer to all the three-point water models? It is as Joao has said - that's just a coordinate file of a pre-equilibrated box of water that was generated using the SPC water model. You can indeed use it to simulate other 3-point water model systems following an initial equilibration. I am trying to see if my protein will be denatured in cold condition. The properties of the water model are going to be critical here. For instance, SPC has a maximum density around -41 C, which is obviously very unphysical (water has a real maximum density at +4 C) so if you're seeking to model behavior at -40 C, then SPC is a very bad choice because its properties are not realistic. I suggest you investigate the many possible water models that exist and find one or more that might reproduce some of the most important properties. None of them gets everything right. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer
Dear Joao, Thank you for your help and the paper link. I was following Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) after the solvation step. So I assume "spc216.gro" refer to all the three-point water models? I am trying to see if my protein will be denatured in cold condition. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, Jun 7, 2017 10:01 PM To: "gromacs.org_gmx-users"; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Simulate protein at subzero condition in aqueous buffer Dear Gromacs, I would like to simulate the protein at subzero condition in aqueous buffer, to see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I ask what is the valid temperature range for water "spc216.gro" ? If I run the simulation at -40 C, does it still assume the system as liquid state instead of frozen state? Thank you. Yours sincerely Cheng -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] RDF of a group around CNT axis
Dear Srinivas, That's absolutely right, I want to calculate the RDF of a certain group around the central axis of a nanotube. And as I know that the RDF of the CNT around its axis is just a sharp peak at the radius, I just tested the command-line parameters for this case, to specify that which command-line should be used. And honestly I do not understand the last sentence of your reply, could you please specify that after isolating the desired group, what command-line I should use? Sincerely, Sajjad On Wed, Jun 7, 2017 at 6:54 PM, SRINIVAS MUSHNOORI < scm...@scarletmail.rutgers.edu> wrote: > If I understand you correctly: you want to calculate the RDF of a certain > group (NOT part of the nanotube) around the central axis of a nanotube? > > The way I do these calculations is to use the gmx trjconv tool to isolate a > trajectory file of ONLY the gropus I am interested in and run my > calculations on that. > If you expect to see one peak but see many that might mean that the RDF is > picking up groups that you don't want it to. > > Hope that helps, > Srinivas > > On Wed, Jun 7, 2017 at 9:41 AM, Sajjad Kavyani > wrote: > > > Dear experts, > > I want to calculate rdf of a certain group around the axis of a cnt, but > I > > do not know what are the proper parameters to choose in the command-line. > > To test the parameters, I calculated the rdf of cnt itself around its > axis > > which must be a sharp peak at the cnt radius. > > I tested the following: (both selection groups of reference and rdf are > > CNT) > > gmx rdf -f md.gro -s md.tpr -o trdf.xvg -xy -selrpos mol_com > > gmx rdf -f md.gro -s md.tpr -o trdf.xvg -xy -selrpos res_com > > gmx rdf -f md.gro -s md.tpr -o trdf.xvg -xy -selrpos whole_res_com > > gmx rdf -f md.gro -s md.tpr -o trdf.xvg -xy -selrpos whole_mol_com > > > > BUT all the results are the same!!! and surprisingly they have multiple > > sharp peaks at different ranges, which I expected just one peak at the > > radius of the CNT > > It is notable that the CNT is aligned to z axis. > > (the first two peaks are listed below): > > > > 0.000 211939.438 > > 0.002 53771.996 > > 0.004 11278.401 > > 0.006 3935.633 > > 0.008 1782.280 > > 0.010 809.616 > > 0.012 584.723 > > 0.014 536.531 > > 0.016 292.361 > > 0.018 149.929 > > 0.020 94.455 > > 0.022 00.000 > > ... > > ... > > ... > > 0.11800.000 > > 0.1200.375 > > 0.1222.212 > > 0.1240.725 > > 0.1266.069 > > 0.128 36.545 > > 0.130 114.868 > > 0.132 278.390 > > 0.134 1669.916 > > 0.136 2360.069 > > 0.138 346.139 > > 0.140 183.770 > > 0.142 39.277 > > > > Could you please explain to me that what should I do? > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdp options in GROMACS 4.5.5
On 6/7/17 10:05 AM, Mohammad Roostaie wrote: Dear Mark, I was using version 5.1.4, but I got this error when using "gmx mdrun": tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted I tried version 5.0.4, too, and I got the same error. Hence, I decided to use the 4.5.5 version which does not give me that error. If you're having a problem with a specific version, you should try something *newer* rather than significantly older. Your posts about that issue went unresolved because there's not nearly enough information about what you did to install 5.1.4 (hardware, OS, compilers, your cmake command, etc). Try with 2016.3 for something modern and actively being maintained. It's a lot more effective for the developers to troubleshoot issues with the current version than one that is not even officially supported any more. -Justin Mohammad From: Mark Abraham To: gmx-us...@gromacs.org; mohammad.r0...@yahoo.com Sent: Wednesday, 7 June 2017, 13:02:46 Subject: Re: [gmx-users] mdp options in GROMACS 4.5.5 Hi,You almost certainly don't want to use version 4.5.5. It's many years old, slow and contains many bugs that have been fixed. Get a new version installed ;-)Mark On Tue, 6 Jun 2017 17:49 João Henriques wrote: Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I mean, not the integration). /J On Tue, Jun 6, 2017 at 5:45 PM, João Henriques wrote: Hi! I'm not sure Verlet was already implemented in GMX 4.5.5, but check the manual for that version (or the closest one). Cheers, /J On Tue, Jun 6, 2017 at 3:27 PM, wrote: Hi All, I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - used as input into grompp to generate em.tpr integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; Short-range electrostatic cut-off rvdw= 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error which said that the cutoff-scheme is not recognized. what should I write instead of "cutoff-scheme" in this version? Thanks,Mohammad -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support /Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer
Hello, "spc216.gro" is not a water model, it's just a pre-equilibrated simulation box (300 K and 1 bar) with the coordinates of 216 3-site water molecules. SPC and TIP3P are two examples of 3-site water models. Water model properties are well studied and tabled (e.g. http://aip.scitation.org/doi/10.1063/1.1862245). I am no expert in pure water simulations, but I doubt 3-site water models can reproduce ice in a realistic way. Will the force field even hold at that temperature? I really don't understand why you'd want to try something like this. However, and to finish, there's one thing I can tell you for sure: your system will be much more "stable" at -40ºC. Why, because it will barely move from it's initial conformation, due to the very low thermal energy. In sum, you'll spend computational time sampling almost nothing. Best regards, João On Wed, Jun 7, 2017 at 4:01 PM, ZHANG Cheng <272699...@qq.com> wrote: > Dear Gromacs, > I would like to simulate the protein at subzero condition in aqueous > buffer, to see if it becomes more stable than the elevated temperature > (e.g. 65 C). Can I ask what is the valid temperature range for water > "spc216.gro" ? If I run the simulation at -40 C, does it still assume the > system as liquid state instead of frozen state? Thank you. > > > Yours sincerely > Cheng > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] RDF of a group around CNT axis
If I understand you correctly: you want to calculate the RDF of a certain group (NOT part of the nanotube) around the central axis of a nanotube? The way I do these calculations is to use the gmx trjconv tool to isolate a trajectory file of ONLY the gropus I am interested in and run my calculations on that. If you expect to see one peak but see many that might mean that the RDF is picking up groups that you don't want it to. Hope that helps, Srinivas On Wed, Jun 7, 2017 at 9:41 AM, Sajjad Kavyani wrote: > Dear experts, > I want to calculate rdf of a certain group around the axis of a cnt, but I > do not know what are the proper parameters to choose in the command-line. > To test the parameters, I calculated the rdf of cnt itself around its axis > which must be a sharp peak at the cnt radius. > I tested the following: (both selection groups of reference and rdf are > CNT) > gmx rdf -f md.gro -s md.tpr -o trdf.xvg -xy -selrpos mol_com > gmx rdf -f md.gro -s md.tpr -o trdf.xvg -xy -selrpos res_com > gmx rdf -f md.gro -s md.tpr -o trdf.xvg -xy -selrpos whole_res_com > gmx rdf -f md.gro -s md.tpr -o trdf.xvg -xy -selrpos whole_mol_com > > BUT all the results are the same!!! and surprisingly they have multiple > sharp peaks at different ranges, which I expected just one peak at the > radius of the CNT > It is notable that the CNT is aligned to z axis. > (the first two peaks are listed below): > > 0.000 211939.438 > 0.002 53771.996 > 0.004 11278.401 > 0.006 3935.633 > 0.008 1782.280 > 0.010 809.616 > 0.012 584.723 > 0.014 536.531 > 0.016 292.361 > 0.018 149.929 > 0.020 94.455 > 0.022 00.000 > ... > ... > ... > 0.11800.000 > 0.1200.375 > 0.1222.212 > 0.1240.725 > 0.1266.069 > 0.128 36.545 > 0.130 114.868 > 0.132 278.390 > 0.134 1669.916 > 0.136 2360.069 > 0.138 346.139 > 0.140 183.770 > 0.142 39.277 > > Could you please explain to me that what should I do? > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdp options in GROMACS 4.5.5
Dear Mark, I was using version 5.1.4, but I got this error when using "gmx mdrun": tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted I tried version 5.0.4, too, and I got the same error. Hence, I decided to use the 4.5.5 version which does not give me that error. Mohammad From: Mark Abraham To: gmx-us...@gromacs.org; mohammad.r0...@yahoo.com Sent: Wednesday, 7 June 2017, 13:02:46 Subject: Re: [gmx-users] mdp options in GROMACS 4.5.5 Hi,You almost certainly don't want to use version 4.5.5. It's many years old, slow and contains many bugs that have been fixed. Get a new version installed ;-)Mark On Tue, 6 Jun 2017 17:49 João Henriques wrote: Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I mean, not the integration). /J On Tue, Jun 6, 2017 at 5:45 PM, João Henriques wrote: > Hi! > > I'm not sure Verlet was already implemented in GMX 4.5.5, but check the > manual for that version (or the closest one). > > Cheers, > > /J > > On Tue, Jun 6, 2017 at 3:27 PM, wrote: > >> Hi All, >> I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - >> used as input into grompp to generate em.tpr >> integrator = steep ; Algorithm (steep = steepest descent >> minimization) >> emtol = 1000.0 ; Stop minimization when the maximum >> force < 1000.0 kJ/mol/nm >> emstep = 0.01 ; Energy step size >> nsteps = 5 ; Maximum number of (minimization) steps >> to perform >> >> ; Parameters describing how to find the neighbors of each atom and how to >> calculate the interactions >> nstlist = 1 ; Frequency to update the neighbor >> list and long range forces >> cutoff-scheme = Verlet >> ns_type = grid ; Method to determine neighbor >> list (simple, grid) >> coulombtype = PME ; Treatment of long range >> electrostatic interactions >> rcoulomb = 1.0 ; Short-range electrostatic >> cut-off >> rvdw = 1.0 ; Short-range Van der Waals >> cut-off >> pbc = xyz ; Periodic Boundary Conditions >> (yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the error >> which said that the cutoff-scheme is not recognized. what should I write >> instead of "cutoff-scheme" in this version? >> Thanks,Mohammad >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support >> /Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. > > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Simulate protein at subzero condition in aqueous buffer
Dear Gromacs, I would like to simulate the protein at subzero condition in aqueous buffer, to see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I ask what is the valid temperature range for water "spc216.gro" ? If I run the simulation at -40 C, does it still assume the system as liquid state instead of frozen state? Thank you. Yours sincerely Cheng -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Doubt about Normal Mode Analysis while scaling nonbonded interactions
Dear all, Is there any way of scaling the Coulombic and/or van der Waals interactions between a protein-ligand system and simultaneously doing Normal Mode analysis on the perturbed system while scaling, perhaps using free-energy code in Gromacs? Thanking in anticipation, Best Regards, Bhagyesh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] RDF of a group around CNT axis
Dear experts, I want to calculate rdf of a certain group around the axis of a cnt, but I do not know what are the proper parameters to choose in the command-line. To test the parameters, I calculated the rdf of cnt itself around its axis which must be a sharp peak at the cnt radius. I tested the following: (both selection groups of reference and rdf are CNT) gmx rdf -f md.gro -s md.tpr -o trdf.xvg -xy -selrpos mol_com gmx rdf -f md.gro -s md.tpr -o trdf.xvg -xy -selrpos res_com gmx rdf -f md.gro -s md.tpr -o trdf.xvg -xy -selrpos whole_res_com gmx rdf -f md.gro -s md.tpr -o trdf.xvg -xy -selrpos whole_mol_com BUT all the results are the same!!! and surprisingly they have multiple sharp peaks at different ranges, which I expected just one peak at the radius of the CNT It is notable that the CNT is aligned to z axis. (the first two peaks are listed below): 0.000 211939.438 0.002 53771.996 0.004 11278.401 0.006 3935.633 0.008 1782.280 0.010 809.616 0.012 584.723 0.014 536.531 0.016 292.361 0.018 149.929 0.020 94.455 0.022 00.000 ... ... ... 0.11800.000 0.1200.375 0.1222.212 0.1240.725 0.1266.069 0.128 36.545 0.130 114.868 0.132 278.390 0.134 1669.916 0.136 2360.069 0.138 346.139 0.140 183.770 0.142 39.277 Could you please explain to me that what should I do? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs
On 6/7/17 8:36 AM, saranya wrote: I have already done simulation for protein and drug interacted protein complexes for 100ns. I just checked out the pressure of my system by using gmx energy command, but the calculated pressure is quite altered (20,000 pressure bar). Moreover, when I calculated the temperature of my system, the result was zero. I am not able to understand the origin of this discrepancy. kindly consider the above issue and please help me out. How are you calculating these properties? Is this directly the output from gmx energy? What were your .mdp settings? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun with multi option
Thank you Mark. Let me explain my scenario here - Umbrella sampling simulations with 15 windows are run using -multi option to obtain PMFs. I have not noticed any issues with the output files (trr, pullf etc.) yet. I have carried out WHAM analysis using gmx wham option and obtained smooth PMFs. Please explain me in which way 'gmx mdrun -multi' option may lead to less reliable with output file and how I can be sure of it. Thanks again. regards, Debdip On 07.06.2017 12:39, Mark Abraham wrote: Hi, gmx mdrun -multidir is a good way to run a group of similar but otherwise uncoupled simulations - they remain uncoupled unless you choose something that couples them, such as replica exchange. gmx mdrun -multi is a bit less reliable with output files. Mark On Wed, Jun 7, 2017 at 12:34 PM Debdip Bhandary < debdip.bhand...@mv.uni-kl.de> wrote: Dear Users, I have doubts regarding simulating multiple systems using mdrun '-multi' option. I have seen that people have used this option for replica exchange (with '-replex' option, of course) where information are exchanged between the systems. In case of different systems (such as different windows in Umbrella sampling simulations, liquid water systems at different temperatures, etc.), as per my understanding (from user manual), there is no exchange of information between the systems and simulations are run without any influence of each other. Am I correct here? or is there any issue when different systems are simulated using -multi/multidir options? Any information regarding this would be appreciated. Thank you in advance. Best regards, Debdip Bhandary -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs
I have already done simulation for protein and drug interacted protein complexes for 100ns. I just checked out the pressure of my system by using gmx energy command, but the calculated pressure is quite altered (20,000 pressure bar). Moreover, when I calculated the temperature of my system, the result was zero. I am not able to understand the origin of this discrepancy. kindly consider the above issue and please help me out. With Regards, *Saranya Vasudevan,* *Research Scholar,* *Molecular Quantum Mechanics Laboratory,* *Department of Physics,* *Bharathiar University,* *Coimbatore-46* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] 3-10 or Pi helices are changing to Alpha over the time: 100 ns MD
Hi Group I have been trying to run a simulation that contains both 3-10 and alpha helical peptides. I am using "AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)" forcefield. Over the course of simulation, the 3-10 helix is changing to alpha as suggested by do_dssp (I am using the newer version of DSSP). Thanx in advance for the help. Regards Prasun PRASUN (ASHOKA) Desire + stability = Resolution Resolution + Hard work = Success -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] number of coordinates does not match after POSRES
Hi Mark, I think I solved the problem. It should be DPOSRES instead of POSRES. The define command should be implemented as "define = -DPOSRES". Finally, the chainX_porse.itp should be included in the master topology file, not chainX-pace.top. Thanks again by the way. Simon 2017-06-07 19:18 GMT+08:00 Simon Kit Sang Chu : > Hi Mark, > > Thanks for your prompt reply. What surprises me is that a change of > "define = POSRES" could cause a problem. The full output from grompp is - > > checking input for internal consistency... > calling cpp... > cpp: error: POSRES: No such file or directory > cpp: warning: ‘-x c’ after last input file has no effect > cpp: fatal error: no input files > compilation terminated. > cpp exit code: 1024 > Tried to execute: 'cpp -I/home/simon/Softs/gromacs-3.3.1/share/gromacs/top > POSRES p1p2.top > gromppDTyNuM' > The 'cpp' command is defined in the .mdp file > processing topology... > processing coordinates... > --- > Program grompp, VERSION 3.3.1 > Source code file: grompp.c, line: 448 > > Fatal error: > number of coordinates in coordinate file (npt.gro, 74787) > does not match topology (p1p2.top, 0) > > > The additional information is attached here as a reference. > > *chainA-pace.top* > [ moleculetype ] > ; Namenrexcl > Protein_A 3 > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass typeB >chargeB massB > 1 N+ 1MET N 10.7 17 ; > qtot 0.7 > . > . > . > 919 922 921 920 20.0 300.0 > > ; Include Position restraint file > #ifdef POSRES > #include "chainA_posre.itp" > #endif > > > *chainA_porse.itp* > ; position restraints for r_1-62_&_Backbone of FullP1P2 in water > > [ position_restraints ] > ; i funct fcxfcyfcz >11 1000 1000 1000 > . > . > . > 5231 1000 1000 1000 > 5301 1000 1000 1000 > > Simon > > > 2017-06-07 16:28 GMT+08:00 Mark Abraham : > >> Hi, >> >> We can't tell, because position restraints are an attribute of >> moleculetypes and those are hidden in your itp files and you didn't share >> which moleculetype grompp reported was the problem. Please copy and paste >> terminal output to make a useful description. >> >> You'll need to include the position restraint file appropriate to each >> moleculetype, of course - not the same one each time. >> >> Mark >> >> On Wed, 7 Jun 2017 08:58 Simon Kit Sang Chu >> wrote: >> >> > Hi, >> > >> > Initially, my topology file can run grompp with .mdp and .gro. However, >> > after putting POSRES in my mdp, the warning "number of coordinates does >> not >> > match" and there is no coordinate recognized in my topology file >> anymore. >> > Therefore, the option POSRES somehow changes everything. >> > >> > The topology file is put here. Is there anything I have written >> > incorrectly? >> > >> > ; Include forcefield parameters >> > #include "ffPACE_1.3.itp" >> > >> > ; Include chain topologies >> > #include "chainA-pace.top" >> > #include "chainB-pace.top" >> > >> > ; Include water topology >> > #include "cgWater.itp" >> > >> > ; Include topology for ions >> > #include "martini_v2.0_ions.itp" >> > >> > [ system ] >> > ; Name >> > FullP1P2 in water >> > >> > [ molecules ] >> > ; Compound#mols >> > Protein_A 1 >> > Protein_B 1` >> > SOL 72899 >> > NA+ 20 >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> > posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> > send a mail to gmx-users-requ...@gromacs.org. >> > >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/Support >> /Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] RMSD analysis
On 6/6/17 4:01 PM, RAHUL SURESH wrote: Dear Justin I think I have confused so much. Let me try to put it in simple way. 1.Can I compare Rmsd , rg , rmsf of protein-ligand complex with that of monomer(just protein) to explain stability? RMSD may be an indicator of something going on but by itself is useless. Rg is only useful if the protein undergoes a large structural change or unfolding. RMSF can be useful if the ensembles are converged; it is subject to big variation if you have any non-equilibrium sampling. 2. Time step of monomer(just protein) simulation is 150ns and protein-ligand complex is 50ns. In this case is it valid to compare the above analyses between monomer and complex? Compare like with like. I wouldn't believe comparisons between single trajectories of differing lengths have any meaning. -Justin Dear Justin I apologise if I am not to your mark to explain in better way. On Wed, 7 Jun 2017 at 1:19 AM, Justin Lemkul wrote: On 6/6/17 1:11 PM, RAHUL SURESH wrote: Dear Justin Thank you. I am considering Rmsd rmsf rg as just supplementary analysis for my study. My aim to analyse conformational change in protein. I would like to bring a note on protein stability after ligand binding. I don't know to which part of monomer I can compare the rmsd of complex with. First 50ns or last .. can you please help me with this? I'm not following. You're talking about monomers and time intervals as if they're interchangeable. What's the story? Do you have a multimer? Are you curious about demonstrating convergence? -Justin On Tue, 6 Jun 2017 at 5:35 PM, Justin Lemkul wrote: On 6/6/17 2:12 AM, RAHUL SURESH wrote: Dear Users *Exp procedure:* I have simulated the protein monomer for 150ns. Using the 150ns conformer, ligand is docked to the protein using autodock and the simulation is carried out for 50ns. *Analysis:* Is it possible to compare my RMSD, RMSF, ROG analysis of complex system with that of monomer? If yes which part of the monomer trajectory should be considered.? This is up to you to determine in light of whatever your goals are in running the simulation. What are you trying to test or determine? Unless the protein's stability is seriously impacted by the ligand, RMSD and Rg are useless. RMSF might be useful if there are motions that are amplified or damped by ligand binding. Run the analysis and see what happens on a per-residue basis. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] number of coordinates does not match after POSRES
On 6/7/17 7:18 AM, Simon Kit Sang Chu wrote: Hi Mark, Thanks for your prompt reply. What surprises me is that a change of "define = POSRES" could cause a problem. The full output from grompp is - checking input for internal consistency... calling cpp... cpp: error: POSRES: No such file or directory Well, here's the first problem. Your syntax is incorrect (#ifdef keywords are prefixed with -D, so "define = POSRES" does nothing but "define = -DPOSRES" would invoke position restraints. cpp: warning: ‘-x c’ after last input file has no effect cpp: fatal error: no input files compilation terminated. cpp exit code: 1024 Tried to execute: 'cpp -I/home/simon/Softs/gromacs-3.3.1/share/gromacs/top POSRES p1p2.top > gromppDTyNuM' The 'cpp' command is defined in the .mdp file processing topology... processing coordinates... --- Program grompp, VERSION 3.3.1 Is there a reason you are using prehistoric, deprecated software? Source code file: grompp.c, line: 448 Fatal error: number of coordinates in coordinate file (npt.gro, 74787) does not match topology (p1p2.top, 0) This suggests mangled syntax, so check for typos, bad line endings, etc. and use a more modern GROMACS version. -Justin The additional information is attached here as a reference. *chainA-pace.top* [ moleculetype ] ; Namenrexcl Protein_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 N+ 1MET N 10.7 17 ; qtot 0.7 . . . 919 922 921 920 20.0 300.0 ; Include Position restraint file #ifdef POSRES #include "chainA_posre.itp" #endif *chainA_porse.itp* ; position restraints for r_1-62_&_Backbone of FullP1P2 in water [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 . . . 5231 1000 1000 1000 5301 1000 1000 1000 Simon 2017-06-07 16:28 GMT+08:00 Mark Abraham : Hi, We can't tell, because position restraints are an attribute of moleculetypes and those are hidden in your itp files and you didn't share which moleculetype grompp reported was the problem. Please copy and paste terminal output to make a useful description. You'll need to include the position restraint file appropriate to each moleculetype, of course - not the same one each time. Mark On Wed, 7 Jun 2017 08:58 Simon Kit Sang Chu wrote: Hi, Initially, my topology file can run grompp with .mdp and .gro. However, after putting POSRES in my mdp, the warning "number of coordinates does not match" and there is no coordinate recognized in my topology file anymore. Therefore, the option POSRES somehow changes everything. The topology file is put here. Is there anything I have written incorrectly? ; Include forcefield parameters #include "ffPACE_1.3.itp" ; Include chain topologies #include "chainA-pace.top" #include "chainB-pace.top" ; Include water topology #include "cgWater.itp" ; Include topology for ions #include "martini_v2.0_ions.itp" [ system ] ; Name FullP1P2 in water [ molecules ] ; Compound#mols Protein_A 1 Protein_B 1` SOL 72899 NA+ 20 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support /Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] number of coordinates does not match after POSRES
Hi Mark, Thanks for your prompt reply. What surprises me is that a change of "define = POSRES" could cause a problem. The full output from grompp is - checking input for internal consistency... calling cpp... cpp: error: POSRES: No such file or directory cpp: warning: ‘-x c’ after last input file has no effect cpp: fatal error: no input files compilation terminated. cpp exit code: 1024 Tried to execute: 'cpp -I/home/simon/Softs/gromacs-3.3.1/share/gromacs/top POSRES p1p2.top > gromppDTyNuM' The 'cpp' command is defined in the .mdp file processing topology... processing coordinates... --- Program grompp, VERSION 3.3.1 Source code file: grompp.c, line: 448 Fatal error: number of coordinates in coordinate file (npt.gro, 74787) does not match topology (p1p2.top, 0) The additional information is attached here as a reference. *chainA-pace.top* [ moleculetype ] ; Namenrexcl Protein_A 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 N+ 1MET N 10.7 17 ; qtot 0.7 . . . 919 922 921 920 20.0 300.0 ; Include Position restraint file #ifdef POSRES #include "chainA_posre.itp" #endif *chainA_porse.itp* ; position restraints for r_1-62_&_Backbone of FullP1P2 in water [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 . . . 5231 1000 1000 1000 5301 1000 1000 1000 Simon 2017-06-07 16:28 GMT+08:00 Mark Abraham : > Hi, > > We can't tell, because position restraints are an attribute of > moleculetypes and those are hidden in your itp files and you didn't share > which moleculetype grompp reported was the problem. Please copy and paste > terminal output to make a useful description. > > You'll need to include the position restraint file appropriate to each > moleculetype, of course - not the same one each time. > > Mark > > On Wed, 7 Jun 2017 08:58 Simon Kit Sang Chu > wrote: > > > Hi, > > > > Initially, my topology file can run grompp with .mdp and .gro. However, > > after putting POSRES in my mdp, the warning "number of coordinates does > not > > match" and there is no coordinate recognized in my topology file anymore. > > Therefore, the option POSRES somehow changes everything. > > > > The topology file is put here. Is there anything I have written > > incorrectly? > > > > ; Include forcefield parameters > > #include "ffPACE_1.3.itp" > > > > ; Include chain topologies > > #include "chainA-pace.top" > > #include "chainB-pace.top" > > > > ; Include water topology > > #include "cgWater.itp" > > > > ; Include topology for ions > > #include "martini_v2.0_ions.itp" > > > > [ system ] > > ; Name > > FullP1P2 in water > > > > [ molecules ] > > ; Compound#mols > > Protein_A 1 > > Protein_B 1` > > SOL 72899 > > NA+ 20 > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun with multi option
Hi, gmx mdrun -multidir is a good way to run a group of similar but otherwise uncoupled simulations - they remain uncoupled unless you choose something that couples them, such as replica exchange. gmx mdrun -multi is a bit less reliable with output files. Mark On Wed, Jun 7, 2017 at 12:34 PM Debdip Bhandary < debdip.bhand...@mv.uni-kl.de> wrote: > Dear Users, > > I have doubts regarding simulating multiple systems using mdrun '-multi' > option. > > I have seen that people have used this option for replica exchange (with > '-replex' option, of course) where information are exchanged between the > systems. In case of different systems (such as different windows in > Umbrella sampling simulations, liquid water systems at different > temperatures, etc.), as per my understanding (from user manual), there > is no exchange of information between the systems and simulations are > run without any influence of each other. Am I correct here? or is there > any issue when different systems are simulated using -multi/multidir > options? Any information regarding this would be appreciated. > > Thank you in advance. > > Best regards, > Debdip Bhandary > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] mdrun with multi option
Dear Users, I have doubts regarding simulating multiple systems using mdrun '-multi' option. I have seen that people have used this option for replica exchange (with '-replex' option, of course) where information are exchanged between the systems. In case of different systems (such as different windows in Umbrella sampling simulations, liquid water systems at different temperatures, etc.), as per my understanding (from user manual), there is no exchange of information between the systems and simulations are run without any influence of each other. Am I correct here? or is there any issue when different systems are simulated using -multi/multidir options? Any information regarding this would be appreciated. Thank you in advance. Best regards, Debdip Bhandary -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] IB Workshop: Bio Visualization with Blender and MembraneEditor (Odense 24.6.2017 )
Hi all! For those of you who are interested in molecular visualization and modeling with Blender and MembraneEditor, we conduct a Hands-on workshop at the Integrative Bioinformatics conference in Odense/University of Southern Denmark! The conference will be 22.-23.6., the workshop at Saturday, 24.6. It consists of 2 parts: - Workshop I: Hands-on Introduction for Beginners - Workshop II: Web-based Bio Visualization and Virtual Reality with Blender More info here: http://cellmicrocosmos.org/index.php/home/cellmicrocosmos-news/236-24-06-2017-biovis-workshop-ib-2017-in-odense There are still seats free! If you want to register, please just contact me directly. Fee for workshop-only participants is 25% of the conference fee. Registration deadline is 15.6.2017 Best wishes, Bjorn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Ramachandran plot
Thank you Dear Mark. Its my pleasure taking your time. ;-) On Wed, Jun 7, 2017 at 2:25 PM, Mark Abraham wrote: > Hi, > > This is why you should actually copy and paste your command lines so you > don't waste your time ;-) And mine. > > Unless you wrote your entire system to your xtc file, your tpr has more > atoms than your xtc, and thus probably some more dihedrals. Make a matching > subset of your tpr using gmx convert-tpr, and use that with gmx rama -s. > > Mark > > On Wed, Jun 7, 2017 at 10:41 AM RAHUL SURESH > wrote: > > > Dear Mark > > Thank you > > > > gmx rama -f traj.xtc -s topol.tpr -o ramachandran.xvg > > > > This was my command.. > > > > I didn't choose any dihedral particularly > > > > > > On Wed, 7 Jun 2017 at 2:00 PM, Mark Abraham > > wrote: > > > > > Hi, > > > > > > Sounds like your choice of dihedrals doesn't match your system. How did > > you > > > select them? > > > > > > Mark > > > > > > On Wed, 7 Jun 2017 08:41 RAHUL SURESH wrote: > > > > > > > Dear Users > > > > > > > > When I try to execute ramachandran plot analysis, I get the following > > > note > > > > like "Dihedral around 5809,5816 not found in topology. Using mult=3" > > > > (nearly 30-40 dihedrals). What is it about? > > > > > > > > Input is just protein structure extended upto 150ns. > > > > > > > > -- > > > > *Regards,* > > > > *Rahul Suresh* > > > > *Research Scholar* > > > > *Bharathiar University* > > > > *Coimbatore* > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > *Regards,* > > *Rahul Suresh* > > *Research Scholar* > > *Bharathiar University* > > *Coimbatore* > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Ramachandran plot
Hi, This is why you should actually copy and paste your command lines so you don't waste your time ;-) And mine. Unless you wrote your entire system to your xtc file, your tpr has more atoms than your xtc, and thus probably some more dihedrals. Make a matching subset of your tpr using gmx convert-tpr, and use that with gmx rama -s. Mark On Wed, Jun 7, 2017 at 10:41 AM RAHUL SURESH wrote: > Dear Mark > Thank you > > gmx rama -f traj.xtc -s topol.tpr -o ramachandran.xvg > > This was my command.. > > I didn't choose any dihedral particularly > > > On Wed, 7 Jun 2017 at 2:00 PM, Mark Abraham > wrote: > > > Hi, > > > > Sounds like your choice of dihedrals doesn't match your system. How did > you > > select them? > > > > Mark > > > > On Wed, 7 Jun 2017 08:41 RAHUL SURESH wrote: > > > > > Dear Users > > > > > > When I try to execute ramachandran plot analysis, I get the following > > note > > > like "Dihedral around 5809,5816 not found in topology. Using mult=3" > > > (nearly 30-40 dihedrals). What is it about? > > > > > > Input is just protein structure extended upto 150ns. > > > > > > -- > > > *Regards,* > > > *Rahul Suresh* > > > *Research Scholar* > > > *Bharathiar University* > > > *Coimbatore* > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Ramachandran plot
Dear Mark Thank you gmx rama -f traj.xtc -s topol.tpr -o ramachandran.xvg This was my command.. I didn't choose any dihedral particularly On Wed, 7 Jun 2017 at 2:00 PM, Mark Abraham wrote: > Hi, > > Sounds like your choice of dihedrals doesn't match your system. How did you > select them? > > Mark > > On Wed, 7 Jun 2017 08:41 RAHUL SURESH wrote: > > > Dear Users > > > > When I try to execute ramachandran plot analysis, I get the following > note > > like "Dihedral around 5809,5816 not found in topology. Using mult=3" > > (nearly 30-40 dihedrals). What is it about? > > > > Input is just protein structure extended upto 150ns. > > > > -- > > *Regards,* > > *Rahul Suresh* > > *Research Scholar* > > *Bharathiar University* > > *Coimbatore* > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulation of pure water
Hi, On Wed, 7 Jun 2017 06:37 G R wrote: > Dear all, > > I want to calculate the relaxation of pure water cell at room temperature > and at freezing point, monitoring its equilibration in volume and in > potential energy. I have 3 question: 1) Can I use packmol for my initial > configuration? Maybe, I don't know. gmx solvate works. if there is any other option,please tell me. 2) Can I use > easily pdb2gmx to generate the topology file? Not really, it's designed for solute in water systems. But you can take any such topology and remove the solute moleculetype and subsections. 3) Which Forcefield is better > for this calculation? > You're not really going to use what is commonly called a force field, but just a water model. There's lots of them, and you should choose one that has been shown to be useful for your kind of study. That's the science part, and your job ;-) Mark I'v already read some tutorial, but if you have any suggestion it woulb be > appreciated. > > Thank you in advance > GR > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] RMSD Matrix Error
Hi, You might want to measure the autocorrelation time of RMSD from your reference structure. Then you'll have an idea how long you have to wait to make a statistically independent observation. Mark On Tue, 6 Jun 2017 08:25 Apramita Chand wrote: > Dear Mark, > Thanks for your reply. I think you're right about the space needed for > generating RMSD Matrix. I definitely was short of 160GB !! > Further, you've talked about me using highly correlated frames and that a > suitable sub-sampling might solve the problem. How would I know which > frames to use? > > > > Message: 2 > Date: Mon, 05 Jun 2017 01:37:37 + > From: Mark Abraham > To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] RMSD Matrix error > Message-ID: > mtnqwgmzf3r+sa-b2qao38ywgw4x9hgplutfu...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > > > > > > > > > > > > > > *On Sun, Jun 4, 2017 at 4:08 PM Apramita Chand > wrote: > Dear All, > > When I'm trying to > construct a RMSD matrix , using the command > g_rms -s protein_equili.gro > -f protein_model1_ut.xtc -m > rmsd-matrix.xpm -tu ns > > I get the > error: > Last frame 20 time 20.000 > > Building RMSD matrix, > 21x21 elements > element 28982; time 2.90 Killed* > > > > That matrix has 4x10^10 elements, each of which needs 4 bytes of memory. > 1GB is about 1x10^9 bytes, so you'd need at least 160 GB of memory. > > The real issue is that you are probably using a large number of highly > correlated frames, so even if you could form the full distance matrix, you > would not learn any more than you would from a matrix formed from a > suitable sub-sampling. > > > > > > *> I have given the reference structure to be the one prior to production > run > and after equilibration step. I have also tried the command with .tpr > file. > Same error! >* > > The problem doesn't change with the nature of the reference structure. > > Mark > > > > yours sincerely, > Apramita > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdp options in GROMACS 4.5.5
Hi, You almost certainly don't want to use version 4.5.5. It's many years old, slow and contains many bugs that have been fixed. Get a new version installed ;-) Mark On Tue, 6 Jun 2017 17:49 João Henriques wrote: > Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I > mean, not the integration). > > /J > > On Tue, Jun 6, 2017 at 5:45 PM, João Henriques < > joao.m.a.henriq...@gmail.com > > wrote: > > > Hi! > > > > I'm not sure Verlet was already implemented in GMX 4.5.5, but check the > > manual for that version (or the closest one). > > > > Cheers, > > > > /J > > > > On Tue, Jun 6, 2017 at 3:27 PM, wrote: > > > >> Hi All, > >> I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - > >> used as input into grompp to generate em.tpr > >> integrator = steep ; Algorithm (steep = steepest descent > >> minimization) > >> emtol = 1000.0; Stop minimization when the maximum > >> force < 1000.0 kJ/mol/nm > >> emstep = 0.01 ; Energy step size > >> nsteps = 5 ; Maximum number of (minimization) steps > >> to perform > >> > >> ; Parameters describing how to find the neighbors of each atom and how > to > >> calculate the interactions > >> nstlist = 1 ; Frequency to update the neighbor > >> list and long range forces > >> cutoff-scheme = Verlet > >> ns_type = grid ; Method to determine neighbor > >> list (simple, grid) > >> coulombtype = PME ; Treatment of long range > >> electrostatic interactions > >> rcoulomb= 1.0 ; Short-range electrostatic > >> cut-off > >> rvdw= 1.0 ; Short-range Van der Waals > >> cut-off > >> pbc = xyz ; Periodic Boundary Conditions > >> (yes/no)Now, I want to use it in GROMACS version 4.5.5. But I got the > error > >> which said that the cutoff-scheme is not recognized. what should I write > >> instead of "cutoff-scheme" in this version? > >> Thanks,Mohammad > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at http://www.gromacs.org/Support > >> /Mailing_Lists/GMX-Users_List before posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy Minimisation
Hi, Please read the advice on system preparation on the GROMACS webpage. You probably have clashing atoms or missing atoms (check all the warnings!) Mark On Tue, 6 Jun 2017 20:19 Pandya, Akash wrote: > Hi all, > > I have used the steepest descent method to minimise my system. It kept > saying certain water molecules could not be settled but it still managed to > reached the maximum force. Then I used the Conjugate gradient method and I > get this error message. Can someday please tell me how I would check and > ultimately get rid of the bad contacts. > > Fatal error: > The coordinates could not be constrained. Minimizer 'cg' can not handle > constraint failures, use minimizer 'steep' before using 'cg'. > > > > Akash > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Ramachandran plot
Hi, Sounds like your choice of dihedrals doesn't match your system. How did you select them? Mark On Wed, 7 Jun 2017 08:41 RAHUL SURESH wrote: > Dear Users > > When I try to execute ramachandran plot analysis, I get the following note > like "Dihedral around 5809,5816 not found in topology. Using mult=3" > (nearly 30-40 dihedrals). What is it about? > > Input is just protein structure extended upto 150ns. > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] number of coordinates does not match after POSRES
Hi, We can't tell, because position restraints are an attribute of moleculetypes and those are hidden in your itp files and you didn't share which moleculetype grompp reported was the problem. Please copy and paste terminal output to make a useful description. You'll need to include the position restraint file appropriate to each moleculetype, of course - not the same one each time. Mark On Wed, 7 Jun 2017 08:58 Simon Kit Sang Chu wrote: > Hi, > > Initially, my topology file can run grompp with .mdp and .gro. However, > after putting POSRES in my mdp, the warning "number of coordinates does not > match" and there is no coordinate recognized in my topology file anymore. > Therefore, the option POSRES somehow changes everything. > > The topology file is put here. Is there anything I have written > incorrectly? > > ; Include forcefield parameters > #include "ffPACE_1.3.itp" > > ; Include chain topologies > #include "chainA-pace.top" > #include "chainB-pace.top" > > ; Include water topology > #include "cgWater.itp" > > ; Include topology for ions > #include "martini_v2.0_ions.itp" > > [ system ] > ; Name > FullP1P2 in water > > [ molecules ] > ; Compound#mols > Protein_A 1 > Protein_B 1` > SOL 72899 > NA+ 20 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Simulation of pure water
Dear all, I want to calculate the relaxation of pure water cell at room temperature and at freezing point, monitoring its equilibration in volume and in potential energy. I have 3 question: 1) Can I use packmol for my initial configuration? if there is any other option,please tell me. 2) Can I use easily pdb2gmx to generate the topology file? 3) Which Forcefield is better for this calculation? I'v already read some tutorial, but if you have any suggestion it woulb be appreciated. Thank you in advanc -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.