[gmx-users] binding delta G, H and S for ion-protein
Dear Justin Very thanks for your guidance. You are right. Excuse me for my several questions. I am beginner in gromacs. If I want to calculate delta H IN potein-ions interaction, can I use g_energy? Is Enthalpy by g_energy exact? Is there a more appropriate tool for calculating delta H in gromacs? Best wishes -- 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] How to calculate RMSD between residues
Hi, i want to calculate rmsd between residue.i searched before posted my query but there is all about rmsf that i know how to calculate. kindly anyone tell me how do i approach this problem. -- With best regards, SIDRA RAFI, Jr.Research Fellow,P-103 Email: sidraraf...@gmail.com, sidra.r...@iccs.edu Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi www.iccs.edu/pcmd/index.php -- 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] binding delta G, H and S for ion-protein
On 2014-03-16 19:05, Andrew Bostick wrote: Dear Justin Thanks for your answer. All of methods you mentioned ( PMF, TI, FEP, BAR) are used for calculating free energy (G). In addition to free energy (G), I want to calculate enthalpy (H) and entropy (S). Are you sure can I use above methods for calculating both of enthalpy (H) and entropy (S)? You can compute H and S by doing a temperature series and use the Van 't Hoff equation. A bit expensive though. Sometimes for well-defined systems if you do a PMF you can subtract the enthalpy coming from the simulation to obtain the entropy. See e.g. PNAS 108 pp. 6838-6842 (2011) Best wishes -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] binding delta G, H and S for ion-protein
On 2014-03-17 09:09, Andrew Bostick wrote: Dear Justin Very thanks for your guidance. You are right. Excuse me for my several questions. I am beginner in gromacs. If I want to calculate delta H IN potein-ions interaction, can I use g_energy? Is Enthalpy by g_energy exact? Is there a more appropriate tool for calculating delta H in gromacs? Best wishes There is only one Delta H for the whole system since it involves volume fluctuations etc. Interaction energies are also difficult. You can find more information on partitioning energies in J. Chem. Theor. Comput. 9 pp. 4542-4551 (2013). -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] Detection of Internal water along MD trajectory
Dear Gromacs users! I've performed md simulation of water soluble protein having water-assessable channel in its interior. I'd like to perform analysis of average number of water molecules detected within the protein interior during MD trajectory with the possible visualization of such internal water binding sites. Does SASA calculation which I've seen in vmd could provide me with additional insights? I'd be thankful if you provide me with some Gromacs or VMD tools suitable for such task. Many thanks for help, James -- 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] Compilation issues with GROMACS 5 beta 2
Hello everyone, my name is Jacek and I am new to GROMACS :) I have recently
downloaded and tried to compile the second beta of GROMACS 5, and run into
some issues along the way, so I decided to ask around and see if I can find
some help. Basically, what I wanted to do was to compile a few different
variants of GROMACS 5 to see how they perform against each other. I was
interested in comparing single and double precision builds, CUDA vs no CUDA
and MPI vs no MPI, in various combinations. Eventually though, I have only
managed to succesfully compile a single-precision, CUDA-extended and
MPI-paralellized build, and none other.
Now to the details:
(1) Compiling with -DGMX_DOUBLE=OFF, -DGMX_MPI=OFF and -DGMX_GPU=OFF
terminates early with a fatal error of lacking MPI headers:
[ 3%] Building C object
src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calc_verletbuf.c.o
In file included from
/media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/legacyheaders/types/commrec.h:40:0,
from
/media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/legacyheaders/coulomb.h:43,
from
/media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/gmxpreprocess/calc_verletbuf.c:49:
/media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/legacyheaders/types/../../utility/gmxmpi.h:62:17:
fatal error: mpi.h: No such file or directory
compilation terminated.
make[2]: ***
[src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calc_verletbuf.c.o]
Error 1
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2
(2) Compiling with -DGMX_DOUBLE=OFF, -DGMX_MPI=OFF and -DGMX_GPU=ON
terminates exactly the same, but after some CUDA stuff is compiled.
(3) Compiling with -DGMX_DOUBLE=OFF, -DGMX_MPI=ON and -DGMX_GPU=OFF
terminates at link with a fatal error of lacking CUDA-specific objects:
[ 92%] Building CXX object
share/template/CMakeFiles/template.dir/template.cpp.o
Linking CXX executable ../../bin/template
../../lib/libgromacs_mpi.so.0.0.0: undefined reference to
`nbnxn_cuda_init_const'
(...some more undefined refs)
../../lib/libgromacs_mpi.so.0.0.0: undefined reference to
`pick_compatible_gpus'
collect2: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2
(4) Compiling with -DGMX_DOUBLE=OFF, -DGMX_GPU=ON and -DGMX_MPI=ON works
fine, as mentioned before.
(5) Compiling with -DGMX_DOUBLE=ON, -DGMX_MPI=OFF and -DGMX_GPU=OFF
terminates identically as (1)
(6) Compiling with -DGMX_DOUBLE=ON, -DGMX_MPI=ON and -DGMX_GPU=OFF
terminates identically as (3)
Each recompilation attempt was made in a fresh direction, with all the files
from a previous build removed, so as to avoid any conflicts. I can post
links to complete compilation logs to PasteBin, if necessary. On the
technical side of things, I am running a 64-bit Ubuntu 12.04 system on a
quad-core i7-860 CPU, with 16GB of RAM and a brand new GTX 780Ti gfx card on
hand-compiled CUDA 5.5 (driver+toolkit).
Of the relevant libs, I have the latest FFTW-3.3.3 compiled nicely in single
('--enable-float --enable-shared --enable-sse2') and double precision
('--enable-shared --enable-sse2') variants stored in separate folders, which
I pass to Cmake through the -DFFTW(F)_LIBRARY parameter. I have OpenMPI
1.4.3.2, MPICH2 and libboost 1.46.1, all from the offical Ubuntu repo.
My guess is that the build system somehow disregards the flags sent to it
and wants MPI/CUDA files even when directly told to skip them. Any ideas on
how to fix/work around this?
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Compilation-issues-with-GROMACS-5-beta-2-tp5015221.html
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Re: [gmx-users] Compilation issues with GROMACS 5 beta 2
Hi
we have fixed quite a few installation issues since beta2. Could you try to
download the latest version from git?
git clone git://git.gromacs.org/gromacs.git
Let us know if you still see the issue.
If you don't have git you can download it from:
https://github.com/gromacs/gromacs/archive/master.zip
Roland
On Mon, Mar 17, 2014 at 8:10 AM, jk broodkil...@gmail.com wrote:
Hello everyone, my name is Jacek and I am new to GROMACS :) I have recently
downloaded and tried to compile the second beta of GROMACS 5, and run into
some issues along the way, so I decided to ask around and see if I can find
some help. Basically, what I wanted to do was to compile a few different
variants of GROMACS 5 to see how they perform against each other. I was
interested in comparing single and double precision builds, CUDA vs no CUDA
and MPI vs no MPI, in various combinations. Eventually though, I have only
managed to succesfully compile a single-precision, CUDA-extended and
MPI-paralellized build, and none other.
Now to the details:
(1) Compiling with -DGMX_DOUBLE=OFF, -DGMX_MPI=OFF and -DGMX_GPU=OFF
terminates early with a fatal error of lacking MPI headers:
[ 3%] Building C object
src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calc_verletbuf.c.o
In file included from
/media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/legacyheaders/types/commrec.h:40:0,
from
/media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/legacyheaders/coulomb.h:43,
from
/media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/gmxpreprocess/calc_verletbuf.c:49:
/media/sda4/soft/struct/gromacs-5.0-beta2/src/gromacs/legacyheaders/types/../../utility/gmxmpi.h:62:17:
fatal error: mpi.h: No such file or directory
compilation terminated.
make[2]: ***
[src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/calc_verletbuf.c.o]
Error 1
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
make: *** [all] Error 2
(2) Compiling with -DGMX_DOUBLE=OFF, -DGMX_MPI=OFF and -DGMX_GPU=ON
terminates exactly the same, but after some CUDA stuff is compiled.
(3) Compiling with -DGMX_DOUBLE=OFF, -DGMX_MPI=ON and -DGMX_GPU=OFF
terminates at link with a fatal error of lacking CUDA-specific objects:
[ 92%] Building CXX object
share/template/CMakeFiles/template.dir/template.cpp.o
Linking CXX executable ../../bin/template
../../lib/libgromacs_mpi.so.0.0.0: undefined reference to
`nbnxn_cuda_init_const'
(...some more undefined refs)
../../lib/libgromacs_mpi.so.0.0.0: undefined reference to
`pick_compatible_gpus'
collect2: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2
(4) Compiling with -DGMX_DOUBLE=OFF, -DGMX_GPU=ON and -DGMX_MPI=ON works
fine, as mentioned before.
(5) Compiling with -DGMX_DOUBLE=ON, -DGMX_MPI=OFF and -DGMX_GPU=OFF
terminates identically as (1)
(6) Compiling with -DGMX_DOUBLE=ON, -DGMX_MPI=ON and -DGMX_GPU=OFF
terminates identically as (3)
Each recompilation attempt was made in a fresh direction, with all the
files
from a previous build removed, so as to avoid any conflicts. I can post
links to complete compilation logs to PasteBin, if necessary. On the
technical side of things, I am running a 64-bit Ubuntu 12.04 system on a
quad-core i7-860 CPU, with 16GB of RAM and a brand new GTX 780Ti gfx card
on
hand-compiled CUDA 5.5 (driver+toolkit).
Of the relevant libs, I have the latest FFTW-3.3.3 compiled nicely in
single
('--enable-float --enable-shared --enable-sse2') and double precision
('--enable-shared --enable-sse2') variants stored in separate folders,
which
I pass to Cmake through the -DFFTW(F)_LIBRARY parameter. I have OpenMPI
1.4.3.2, MPICH2 and libboost 1.46.1, all from the offical Ubuntu repo.
My guess is that the build system somehow disregards the flags sent to it
and wants MPI/CUDA files even when directly told to skip them. Any ideas on
how to fix/work around this?
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Compilation-issues-with-GROMACS-5-beta-2-tp5015221.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
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* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
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865-241-1537, ORNL PO BOX 2008 MS6309
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Re: [gmx-users] Compilation issues with GROMACS 5 beta 2
Dear Roland, many thanks for that advice! I cloned the git repo (as of commit b4619a45f3643c963c30b295eeec580882dd915a) and all my use cases are compiling perfectly now. I still have to test how they actually work, but I'm definitely a step forward in the right direction. -- View this message in context: http://gromacs.5086.x6.nabble.com/Compilation-issues-with-GROMACS-5-beta-2-tp5015221p5015223.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] constraint pulling
Dear gromacs users I will use pull = constraint (constraint pulling) for PMF calculations. There is a tutorial about PMF from Justin in which he used pull = umbrella (umbrella sampling). In justin tutorial, step are as follows: 1) preparation of system 2) minimization equilibration 3) generate configuration 4) umbrella sampling 5) WHAM which gives PMF curve I conceive in my case (pull = constraint), steps 1, 2 and 3 are similar to justin case (pull = umbrella). Since, WHAM analyzes output files generated by umbrella sampling, I have not idea about steps 4 and 5. I did not know how to obtain PMF curve in my case. If my notion is wrong, please give me more explanation such that I do this PMF calculation using constraint pulling method. Please tell me steps needed for constraint pulling. Is there a tutorial about PMF calculation using constraint pulling method? Any help will highly appreciated -- 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] free energy calculations
three questions regarding free energy calculations ... 1) i try running a free energy calculation and get an error msg: The Verlet cut-off scheme does not (yet) support free-energy calculations with perturbed atoms, only perturbed interactions. This will be implemented soon. Use the group scheme for now. in my top file i simply defined typeB, chargeB, massB for a particular molecule, my mdp file is below ... what is the difference between perturbed interactions and perturbed atoms?? 2) if i turn OFF a molecule turning all atoms in this molecule into dummy types with zero charge and vdw epsilon=0 ... do i have to explicitely tell gmx about the bonded-interactions between the various dummy atoms, or is gmx smart enough to simply use the original parameters from the un-perturbed molecule? does couple-moltype help here ?? 3) is there anywhere such a thing as a tutorial for advanced free energy methods, in particular i'd be interested in trying expanded ensembles/hamiltonian exchange ... thanks! michael mdp file: integrator = sd dt = 0.002 nsteps = 10 comm-grps= System ; nstxout = 100 nstvout = 0 nstfout = 0 nstlog = 100 nstenergy= 100 ; nstlist = 20 ns_type = grid pbc = xyz cutoff-scheme= Verlet ; coulombtype = PME rcoulomb = 1.2 vdw_type = cut-off rvdw = 1.2 DispCorr = No ; tc-grps = Other wat tau_t= 0.2 0.2 ref_t= 298.0 298.0 ; gen-vel = yes gen-temp = 40.0 gen-seed = 45411 continuation = no ; Pcoupl = berendsen Pcoupltype = anisotropic tau_p= 0.4 0.4 0.4 0.0 0.0 0.0 compressibility = 1.0e-5 1.0e-5 1.0e-5 0.0 0.0 0.0 ref_p= 1.0 1.0 1.0 0.0 0.0 0.0 ; constraints = h-bonds constraint-algorithm = LINCS ; free-energy = yes init-lambda-state= 0 delta-lambda = 0 coul-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 vdw-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 calc-lambda-neighbors= -1 sc-alpha = 0.002 sc-r-power = 48 sc-coul = yes sc-power = 1 sc-sigma = 0.3 nstdhdl = 100 -- View this message in context: http://gromacs.5086.x6.nabble.com/free-energy-calculations-tp5015229.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] binding delta G, H and S for ion-protein
Dear Board, I have done this with a steered MD, using covarience, etc...in the end there are nice delG and H,S line graphs...the only argument I have heard however is when doing the subtraction the third curve always gives the correct repective energy change, but the delG line graph may not always represent the energy path correctly as there becomes a large amount of overlap in energy changes between other groups not in the index grp used (ions, h2o, long range effects lowering conformational states such as a 3 water bridge to another protein) ...only making it much more cumbersome, or making the delS or H have much higher STDV or total error that can for a biochemist looking at say a small ligand binding energy squirm (delG say of 20 kCal/mol but STDV or error at +/- 10 kCal/mol where say a protein protein or DNA interaction may have dips and wells in the 100s of kCal/mol range so not quite as problematic...all assuming one is not using a QQMM where the errors go down one or two orders ofmagnitude)...theH/S pathways though can be informative especially for biologist looking at macromolecules...I would be interested in opinions/thoughts on these differences though... Stephan Watkins Gesendet:Montag, 17. Mrz 2014 um 09:26 Uhr Von:David van der Spoel sp...@xray.bmc.uu.se An:gmx-us...@gromacs.org Betreff:Re: [gmx-users] binding delta G, H and S for ion-protein On 2014-03-16 19:05, Andrew Bostick wrote: Dear Justin Thanks for your answer. All of methods you mentioned ( PMF, TI, FEP, BAR) are used for calculating free energy (G). In addition to free energy (G), I want to calculate enthalpy (H) and entropy (S). Are you sure can I use above methods for calculating both of enthalpy (H) and entropy (S)? You can compute H and S by doing a temperature series and use the Van t Hoff equation. A bit expensive though. Sometimes for well-defined systems if you do a PMF you can subtract the enthalpy coming from the simulation to obtain the entropy. See e.g. PNAS 108 pp. 6838-6842 (2011) Best wishes -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Cant 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] CELLmicrocosmos 2.2.2_1 MembraneEditor Minor Release
Dear Colleagues, the next minor release is out now: ** CELLmicrocosmos 2.2.2_1 MembraneEditor Minor Release ** *Molecule Alignment and Performance Update, Bugfixes (17.03.2014)* Shortly, here the number of improvements and bug fixes: - All users of Linux distributions usind IcedTea for Java WebStart will be happy: the actual release was pre-compiled with Java 6 and it is not required anymore to install some alternative packages. - The direct APL@Voro integration did not work on all systems correctly, this problem is fixed now. - The lipid/protein alignment mode was extended. First, the area can be defined in which molecular structures around the molecule to align are shown. Second, the alignment can be manually changed by providing an axis-angle. - For all those people who want to work with a larger number of molecular structures, a special mode was implemented based on work done during Philipp Unruh's diploma thesis. You will find it in the 3D Settings dialog. Just restart the WebStart version of the MembraneEditor or install it from here: http://Cm2.CELLmicrocosmos.org Happy Modeling! Björn Sommer team.CELLmicrocosmos.org -- Björn Sommer CELLmicrocosmos.org Cell Modeling Visualization Bio-/Medical Informatics Group Faculty of Technology Bielefeld University Germany e-m bjo...@cellmicrocosmos.org h-p www.CELLmicrocosmos.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] How can I concatenate multiple g96 configurations into a single trajectory?
Hi, I have been creating several .g96 configuration files by hand (actually, using a scripting language). I like .g96 as a configuration file format because it provides 9 decimal places of precision for the x, y, and z coordinates of the position and velocity of atoms in my system -- whereas .gro and .pdb configuration file formats offer much lower precision. My system is crystalline, and I found many months ago that the lower precision offered by .gro and .pdb is not quite enough to achieve the exact bond lengths that I want in my crystal. Many months ago, Professor van der Spoel suggested on this list that I switch to .g96 for my configurations. So for many months I have been successfully using .g96 configurations as input to grompp to make the .tpr files necessary for simulation. Today, however, I am trying to do something somewhat unusual, and I run into an unusual problem. Suppose I have made three .g96 configurations by hand: conf1.g96, conf2.g96, and conf3.g96. I want to compute the single-point energy of all three configurations. (Why would I want to do this? I have written code in a scripting language to generate frames in which a particular angle is scanned from one extreme to the other; I want to use Gromacs to simply compute the single-point energy at each frame in the scan, without taking any MD moves.) One way to do this might be to run three different zero-step MD simulations, by passing the three configurations separately to grompp, obtaining three separate .tpr files, and passing those three .tpr files to mdrun. But this documentation page http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy warns that zero-step MD simulations have complications related to catering to possible restarts and is not recommended. Doing it that way is also a little inconvenient because eventually I will have dozens or hundreds of separate handmade .g96 configurations for which to calculate the single-point energy, and running hundreds of zero-step simulations would probably require some sort of bash script. So, my thought is to concatenate the three (or more) .g96 configurations into a single trajectory, and then feed that trajectory to the -rerun switch of mdrun to compute the energy of each frame. My question is, how can I concatenate three (or more) .g96 configurations into a single trajectory of any type? I have tried: trjcat -f conf1.g96 conf2.g96 conf3.g96 -o output.trr But I get this error message: --- Program trjcat, VERSION 4.5.5 Source code file: trxio.c, line: 693 Fatal error: Reading trajectories in .g96 format is broken. Please use a different file format. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Reading trajectories in .g96 format may be broken, but reading CONFIGURATIONS in .g96 is not broken, as far as I know (I routinely pass g96 configurations to the -c switch of grompp). Is there any other way I can concatenate three (or more) .g96 configurations into a single trajectory of any type (.trr, .xtc, etc) -- WITHOUT going through .gro or .pdb (e.g., by converting from .g96 using editconf), which have lower precision? Thanks so much for your time! Andrew DeYoung Carnegie Mellon University -- 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] How can I concatenate multiple g96 configurations into a single trajectory?
Hi Andrew, You can convert each frame to trr and concatenate those. Cheers, Tsjerk On Mar 17, 2014 8:18 PM, Andrew DeYoung adeyo...@andrew.cmu.edu wrote: Hi, I have been creating several .g96 configuration files by hand (actually, using a scripting language). I like .g96 as a configuration file format because it provides 9 decimal places of precision for the x, y, and z coordinates of the position and velocity of atoms in my system -- whereas .gro and .pdb configuration file formats offer much lower precision. My system is crystalline, and I found many months ago that the lower precision offered by .gro and .pdb is not quite enough to achieve the exact bond lengths that I want in my crystal. Many months ago, Professor van der Spoel suggested on this list that I switch to .g96 for my configurations. So for many months I have been successfully using .g96 configurations as input to grompp to make the .tpr files necessary for simulation. Today, however, I am trying to do something somewhat unusual, and I run into an unusual problem. Suppose I have made three .g96 configurations by hand: conf1.g96, conf2.g96, and conf3.g96. I want to compute the single-point energy of all three configurations. (Why would I want to do this? I have written code in a scripting language to generate frames in which a particular angle is scanned from one extreme to the other; I want to use Gromacs to simply compute the single-point energy at each frame in the scan, without taking any MD moves.) One way to do this might be to run three different zero-step MD simulations, by passing the three configurations separately to grompp, obtaining three separate .tpr files, and passing those three .tpr files to mdrun. But this documentation page http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy warns that zero-step MD simulations have complications related to catering to possible restarts and is not recommended. Doing it that way is also a little inconvenient because eventually I will have dozens or hundreds of separate handmade .g96 configurations for which to calculate the single-point energy, and running hundreds of zero-step simulations would probably require some sort of bash script. So, my thought is to concatenate the three (or more) .g96 configurations into a single trajectory, and then feed that trajectory to the -rerun switch of mdrun to compute the energy of each frame. My question is, how can I concatenate three (or more) .g96 configurations into a single trajectory of any type? I have tried: trjcat -f conf1.g96 conf2.g96 conf3.g96 -o output.trr But I get this error message: --- Program trjcat, VERSION 4.5.5 Source code file: trxio.c, line: 693 Fatal error: Reading trajectories in .g96 format is broken. Please use a different file format. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Reading trajectories in .g96 format may be broken, but reading CONFIGURATIONS in .g96 is not broken, as far as I know (I routinely pass g96 configurations to the -c switch of grompp). Is there any other way I can concatenate three (or more) .g96 configurations into a single trajectory of any type (.trr, .xtc, etc) -- WITHOUT going through .gro or .pdb (e.g., by converting from .g96 using editconf), which have lower precision? Thanks so much for your time! Andrew DeYoung Carnegie Mellon University -- 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] How can I concatenate multiple g96 configurations into a single trajectory?
Hi Tsjerk, Thanks so much for your time. Unfortunately, when I tried to convert a .g96 configuration to a .trr trajectory, with this command: trjconv -f conf1.g96 -o conf1.trr I get this error message: --- Program trjconv_d, VERSION 4.5.5 Source code file: trxio.c, line: 693 Fatal error: Reading trajectories in .g96 format is broken. Please use a different file format. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I am running Gromacs 4.5.5. Do you know if there is another way to convert a .g96 configuration to a .trr trajectory, without using trjconv? Or do you know if a different version of Gromacs would not have this problem? Thanks for your time. Andrew DeYoung Carnegie Mellon University -- 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] How can I concatenate multiple g96 configurations into a single trajectory?
On 3/17/14, 6:45 PM, Andrew DeYoung wrote: Hi Tsjerk, Thanks so much for your time. Unfortunately, when I tried to convert a .g96 configuration to a .trr trajectory, with this command: trjconv -f conf1.g96 -o conf1.trr I get this error message: --- Program trjconv_d, VERSION 4.5.5 Source code file: trxio.c, line: 693 Fatal error: Reading trajectories in .g96 format is broken. Please use a different file format. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I am running Gromacs 4.5.5. Do you know if there is another way to convert a .g96 configuration to a .trr trajectory, without using trjconv? Or do you know if a different version of Gromacs would not have this problem? Anything in the 4.6 series or newer should work. The reading of .g96 was disabled in 2011 when there were problems, but then reinstated in late 2012, before the release of the first 4.6 beta release. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] PEG residue
I am new to GROMACS. I am trying to use pdb2gmx to create a topology for PEG (O-C-C)n with only H on one terminal and OH on the other. I know that I need to add a residue entry to the forcefield for example to aminoacids.rtp in the gromos54a7.ff folder. However, I do not know how to construct the residue entry. I do know the format but I do not know what values to enter for bonds, angles, dihedrals ect. Can anyone help me? -- View this message in context: http://gromacs.5086.x6.nabble.com/PEG-residue-tp5015237.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] PEG residue
On 3/17/14, 7:05 PM, dan42 wrote: I am new to GROMACS. I am trying to use pdb2gmx to create a topology for PEG (O-C-C)n with only H on one terminal and OH on the other. I know that I need to add a residue entry to the forcefield for example to aminoacids.rtp in Well, multiple residues actually, to account for terminal and repeating block residues. http://www.gromacs.org/Documentation/How-tos/Polymers the gromos54a7.ff folder. However, I do not know how to construct the residue entry. I do know the format but I do not know what values to enter for bonds, angles, dihedrals ect. Can anyone help me? Parameters for alkanes are pretty much cut-and-paste from any residue that has CH2-CH2 linkages, in addition to the CH2-O-H groups at the ends. You can take the gb_*, ga_*, and gd_* parameters that you need based on what you find in ffbonded.itp - parameters are described in some detail there. The problem you will have is the ether linkages. AFAIK there are no parameters for ethers in 54A7, though other related force field parameter sets (i.e., those for sugars) will have them. The Gromos parameter sets are all closely linked, so the parametrization protocol should yield reasonably compatible parameters. It's something you will want to check thoroughly. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] asking for N and C termini for DNA and giving error
Thanks Justin. I have very recently started doing MD, guided by Gromacs tutorials; not aware of this issue. Thanks for you suggestion, I will try with Amber ff. Sucharita Dey,PhD, Research Fellow, Cancer Science Institute of Singapore, National University of Singapore. 14, Medical Drive, #12-01, Singapore 117599. Tel: (65) 90355220, email: cs...@nus.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul [jalem...@vt.edu] Sent: Monday, March 17, 2014 7:49 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] asking for N and C termini for DNA and giving error On 3/16/14, 11:35 PM, Sucharita Dey wrote: Hello, Thanks Justin. Since my protein has a modified DNA residue (methyl cytosine) I have copied the gromos53a6.ff folder as well as the residuetypes.dat file in my working directory and modified them, where I have inserted my modified DNA residue as DNA and also have renamed DADE, DTHY ... as DNA. Within gromos53a6.ff, following Adding a new residue from gmx-tutorial, I have modified .rtp, .hdb, atomtypes.atp, and residuetypes.dat. In the rtp, hdb files as well DNA is written as DADE, DTHY And I am choosing this force field from the current directory while running pdb2gmx. It is not giving error for the modified residue but giving error for DNA terminal. Am I missing anything for which it is not identifying the DNA as DNA? The Gromos96 53A6 force field does not have termini database entries for DNA or RNA, so the nucleic acids are not fully functional. I don't know why you chose this parameter set, but the nucleic acid parameters are far surpassed (in terms of quality) by other force fields like AMBER and CHARMM. I would recommend you use one of those, instead. They are also fully functional within Gromacs. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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. -- 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.
