[gmx-users] Domain decomposition error in alchemical free energy perturbation MD
Dear all,
I'm doing an slow-growth alchemical free energy perturbation calculation
of the formation of a disulfide bridge between two Cysteines with Gromacs.
I've had tried different ways to combine the topology of both state A and
state B, and finally settled with the most direct way -- to mutate the
atoms that have different partial charges in the two states, and transform
the two hydrogen atoms into dummy atoms. As suggested by Gromacs manual
and some messages from the internet, I put explicitly the OPLS parameters
for the bonds, pairs, angles and dihedrals changed from state A to state B,
and the grompp didn't give a warning. But when I was testing the production
simulation on two processors, there was a warning of fatal error in the log
file:
=
Initializing Domain Decomposition on 2 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 3.774 nm, LJC Pairs NB, atoms 12 205
multi-body bonded interactions: 0.640 nm, Ryckaert-Bell., atoms 1013 417
Minimum cell size due to bonded interactions: 4.151 nm
Using 0 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 2 cells with a minimum initial size of 5.189 nm
The maximum allowed number of cells is: X 0 Y 0 Z 0
---
Program mdrun, VERSION 4.5.4
Source code file: domdec.c, line: 6436
Fatal error:
There is no domain decomposition for 2 nodes that is compatible with the
given box and a minimum cell size of 5.18876 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
=
The atoms indexed 12 and 205 are a CD1 in Leu1 and another CB in Ala12
respectively. I checked the topology and found no entries containing both
these atoms. What's weird is that there's no way for these two atoms to have
bonded interactions, but it says in the log that they have a two-body bonded
interaction with a distance of 3.774 nm, which I cannot understand.
Does anyone have an explanation what this could mean? Any suggestion is
appreciated!
Thanks in advance!
Xiaoxiao He
Oct. 15, 2011
Attached are the input parameters for the production md:
=
-Input Parameters:
integrator = sd
nsteps = 200
init_step= 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 10
comm_mode= Linear
nstlog = 100
nstxout = 10
nstvout = 10
nstfout = 10
nstcalcenergy= 10
nstenergy= 100
nstxtcout= 1000
init_t = 0
delta_t = 0.0005
xtcprec = 1000
nkx = 36
nky = 36
nkz = 36
pme_order= 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = No
nsttcouple = -1
epc = Berendsen
epctype = Isotropic
nstpcouple = 10
tau_p= 1
ref_p (3x3):
ref_p[0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 4.5e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed= 815131
rlist= 1.3
rlistlong= 1.3
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.3
vdwtype = Switch
rvdw_switch = 0.8
rvdw = 0.9
epsilon_r= 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
[gmx-users] How to obtain and how to use acpype
Dear gromacs users I want to do MD simulation of protein-ligand. I read a tutorial by John E. Kerrigan Tutorial for Trypsin-Benzamidine complex molecular dynamics study. in which they used acpype. I want to know what is acpype? a program in gromacs or amber or a pythone file? please explain about that more. How to obtain and how to use acpype? Any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to obtain and how to use acpype
I dont know the details but this link may be useful. http://code.google.com/p/acpype/ Kavya On Sat, Oct 15, 2011 at 2:01 PM, leila karami karami.lei...@gmail.comwrote: Dear gromacs users I want to do MD simulation of protein-ligand. I read a tutorial by John E. Kerrigan Tutorial for Trypsin-Benzamidine complex molecular dynamics study. in which they used acpype. I want to know what is acpype? a program in gromacs or amber or a pythone file? please explain about that more. How to obtain and how to use acpype? Any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to obtain and how to use acpype
Dear Kavya Thanks for your attention Unfortunately, I don't access to http://code.google.com/p/acpype/ Your client does not have permission to get URL /p/acpype/ from this server. Please guide me. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Link to Intel MKL (fftw) via cmake options
On 10/15/2011 1:15 AM, Mark Abraham wrote:
I use
ccmake ..\
-DGMX_FFT_LIBRARY=mkl \
-DMKL_LIBRARIES=${MKL}/lib/em64t/libmkl_intel_thread.so;${MKL}/lib/em64t/libmkl_lapack.so;${MKL}/lib/em64t/libmkl_core.so;${MKL}/lib/em64t/libmkl_em64t.a;${MKL}/lib/em64t/libguide.so;/usr/lib64/libpthread.so
\
-DMKL_INCLUDE_DIR=${MKL}/include\
-DGMX_MPI=ON\
-DGMX_THREADS=OFF
Thanks for your hints, I made it now through `cmake` with:
--- 8 --- [cut here] --
GMXVERSION=gromacs-4.5.5
GMXTARGET=/opt/gromacs455
MINC=/opt/intel/composerxe/mkl/include
MLIB=/opt/intel/composerxe/mkl/lib/intel64
ILIB=/opt/intel/composerxe/lib/intel64
LLIB=/usr/lib64
export CXX=icpc
export CC=icc
cmake ../$GMXVERSION \
-DGMX_FFT_LIBRARY=mkl
-DMKL_LIBRARIES=${MLIB}/libmkl_intel_ilp64.so;${MLIB}/libmkl_core.so;${MLIB}/libmkl_intel_thread.so;${ILIB}/libiomp5.so;${LLIB}/libpthread.so\
-DMKL_INCLUDE_DIR=${MINC} \
-DGMX_MPI=OFF \
-DGMX_THREADS=ON \
-DCMAKE_INSTALL_PREFIX=${GMXTARGET} \
-DGMX_X11=OFF\
-DGMX_BINARY_SUFFIX=_t
---
on `make`, there are still some compiler flag related
problems. The cmake scripts invoked by the command
above identified the Intel64 compiler and guessed
'almost correct' optimization and code-generation options:
(Compiler: /opt/intel/composer_xe_2011_sp1.6.233/bin/intel64/ic*)
--- [CMakeCache.txt] -
...
//Flags used by the compiler during all build types
CMAKE_CXX_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99 '
//Flags used by the compiler during release builds.
CMAKE_CXX_FLAGS_RELEASE:STRING=-mtune=itanium2 -mtune=core2 -O3 -DNDEBUG
//Flags used by the compiler during all build types
CMAKE_C_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99 '
//Flags used by the compiler during release builds.
CMAKE_C_FLAGS_RELEASE:STRING=-mtune=itanium2 -mtune=core2 -O3 -DNDEBUG
...
These are obviously the wrong flags for the detected architecture,
sse2 is no longer available and so are the the mtune architectures.
The correct options for the actual compiler for Intel64 would read:
CMAKE_CXX_FLAGS:STRING=' -msse3 -ip -funroll-all-loops -std=gnu99 '
CMAKE_CXX_FLAGS_RELEASE:STRING=-O3 -DNDEBUG
CMAKE_C_FLAGS:STRING=' -msse3 -ip -funroll-all-loops -std=gnu99 '
CMAKE_C_FLAGS_RELEASE:STRING=-O3 -DNDEBUG
Even with the wrong options, the `make` would eventually succeed
with some option-warnings but without error.
But the install is broken. On `make install-mdrun`, the scripts would
remove any library from src/gmxlib/CMakeFiles/CMakeRelink.dir
and bail out with the error below. Even if you copy the libraries
by hand to CMakeRelink.dir/, the'll get removed by make install-mdrun
before trying to link with them.
--- [cat errmsg.txt] -
[ 70%] Built target gmx
[ 89%] Built target md
[ 98%] Built target gmxpreprocess
[100%] Built target mdrun
[100%] Installing mdrun
-- Install configuration: Release
-- Install component: libraries
CMake Error at /x/y/Gromacs/build/src/gmxlib/cmake_install.cmake:38 (FILE):
file INSTALL cannot find
/x/y/Gromacs/build/src/gmxlib/CMakeFiles/CMakeRelink.dir/libgmx.so.6.
Still broken with the new Intel Compiler but probably close ;-)
Thanks and regards,
r^b
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] Domain decomposition error in alchemical free energy perturbation MD
On Sat, Oct 15, 2011 at 2:11 PM, Xiaoxiao He xxia...@ust.hk wrote:
Dear all,
I'm doing an slow-growth alchemical free energy perturbation calculation
of the formation of a disulfide bridge between two Cysteines with Gromacs.
I've had tried different ways to combine the topology of both state A and
state B, and finally settled with the most direct way -- to mutate the
atoms that have different partial charges in the two states, and transform
the two hydrogen atoms into dummy atoms. As suggested by Gromacs manual
and some messages from the internet, I put explicitly the OPLS parameters
for the bonds, pairs, angles and dihedrals changed from state A to state B,
and the grompp didn't give a warning. But when I was testing the production
simulation on two processors, there was a warning of fatal error in the log
file:
=
Initializing Domain Decomposition on 2 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 3.774 nm, LJC Pairs NB, atoms 12 205
multi-body bonded interactions: 0.640 nm, Ryckaert-Bell., atoms 1013 417
Minimum cell size due to bonded interactions: 4.151 nm
Using 0 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 2 cells with a minimum initial size of 5.189 nm
The maximum allowed number of cells is: X 0 Y 0 Z 0
---
Program mdrun, VERSION 4.5.4
Source code file: domdec.c, line: 6436
Fatal error:
There is no domain decomposition for 2 nodes that is compatible with the
given box and a minimum cell size of 5.18876 nm
Change the number of nodes or mdrun option -rdd or -dds
as suggested by the log:
1] Change the number of nodes
or
2] mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
=
The atoms indexed 12 and 205 are a CD1 in Leu1 and another CB in Ala12
respectively. I checked the topology and found no entries containing both
these atoms. What's weird is that there's no way for these two atoms to have
bonded interactions, but it says in the log that they have a two-body bonded
interaction with a distance of 3.774 nm, which I cannot understand.
Does anyone have an explanation what this could mean? Any suggestion is
appreciated!
Thanks in advance!
Xiaoxiao He
Oct. 15, 2011
Attached are the input parameters for the production md:
=
-Input Parameters:
integrator = sd
nsteps = 200
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 10
comm_mode = Linear
nstlog = 100
nstxout = 10
nstvout = 10
nstfout = 10
nstcalcenergy = 10
nstenergy = 100
nstxtcout = 1000
init_t = 0
delta_t = 0.0005
xtcprec = 1000
nkx = 36
nky = 36
nkz = 36
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = No
nsttcouple = -1
epc = Berendsen
epctype = Isotropic
nstpcouple = 10
tau_p = 1
ref_p (3x3):
ref_p[ 0]={ 1.0e+00, 0.0e+00, 0.0e+00}
ref_p[ 1]={ 0.0e+00, 1.0e+00, 0.0e+00}
ref_p[ 2]={ 0.0e+00, 0.0e+00, 1.0e+00}
compress (3x3):
compress[ 0]={ 4.5e-05, 0.0e+00, 0.0e+00}
compress[ 1]={ 0.0e+00, 4.5e-05, 0.0e+00}
compress[ 2]={ 0.0e+00, 0.0e+00, 4.5e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.0e+00
posres_com[1]= 0.0e+00
posres_com[2]= 0.0e+00
posres_comB (3):
posres_comB[0]= 0.0e+00
posres_comB[1]= 0.0e+00
posres_comB[2]= 0.0e+00
andersen_seed = 815131
rlist = 1.3
rlistlong = 1.3
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.3
vdwtype = Switch
[gmx-users] how to calculate the normal of plane for Tryptophan or how to get the comparison matrix in g_rms
I send this message yesterday, but I myself donot see this message, so, I send it again, very sorry for the spam. Dear gmxer's I am simulating a protein, want to calculate the normal of plane for Tryptophan residue amino acid in that protein. We need to take into account that, in simulation, atoms of TRP vibrate all the time, and they are not always on the same plane: If they were on the same plane in my simulation, to calculate the normal would be rather straighforward. As those atoms are not on the same plane, I think my calculation should be something like least square fitting. I look at g_rms command, and plan to calculate the normal in following steps: 1. create a Tryptophan with ideal configuration, where all 8 C atom and N atom (except CB atom) should be in the same plane, I put these 9 atoms in xy plane, and the normal of this TRP molecule is just z axis 2.I then calculate the rms between the TRP residue in my simulation and that ideal TRP molecule 3.If I know the rotate matrix (e.g. how to rotate the TRP in my simulation in the least-squares fitting of rms calculation), then I just rotate z axis (0,0,1) back ( in other words, multiple z axis (0,0,1) with the inverse of that rotate matrix) to get the plane normal for TRP in my simulation. So, I am wondering how to know the the rotate matrix when g_rms do the least-squares fitting? Is that in the comparison matrix dumped by the -bin option? If so, how to read the rotate matrix from that binary file produced by -bin option? Or, if there is other way that I can calculate plane normal for TRP? Thank you so much for your kind help. yours xiaodong school of chem, ANU -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] would trjcat correctly delete extra frames?
Hi all, I am doing simulations on cluster piece by piece with -maxh and -noappend options of mdrun. However, one piece crushed way before approaching the max hours for unknown reasons. As a result, the part0004.trr file contains a couple of frames ahead of part0004.cpt file, since the most .cpt was only written about 5 or 10 minutes before the crush. So I plan to continue with the part0004.cpt file, and I expect the part0005.trr file I will get would have its initial 3 or 4 frames duplicated (only # steps and time) with the last 3 or 4 frames in part0004.trr file. And when I concatenate them together with trjcat, would the last 3 or 4 frames in part0004.trr file be automatically deleted? and only the initial 3 or 4 frames in part0005.trr be included in the resulting .trr file? Thanks for any suggestion! Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Normal Mode Analysis
Thanks It's works fine but I'venot find significant increasing in the simulation speed :) but I'd also to test MPI. Could you tell me what exactly ( MPI or threading) might provide better productivity in case of big heterogenious system ( e.g protein in membrane )? James 2011/10/15 lina lina.lastn...@gmail.com On Sat, Oct 15, 2011 at 2:58 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs users! I have couple of questions about some Gromacs features. 1- I'm looking for tutorial where I could find clear example of force fied based Normal Mode Analysis via Gromacs E.g on first step I would like to prepare structure of my protein in pereodic boundary conditions and conduct energy minimization ( I've already can do it). Next I'd like to conduct full-atomic Normal Mode analysis and obtain motion trajectories along some lowest frequency modes for futher visualization in VMD. Finally I'd like to obtain information about frequencies ( eigenvalues) of each mode as well as frequencies of each residue fluctuations along different modes. 2- Also I'm looking for possible ways to enhanse Gromacs efficiency eg via ussage of multi cores of my CPU. I've found possible sillution via MPI function but this way dowsnt work in my case. How I can activate hyperthreading function as well as other possible ways ? If you installed from src, during configure --enable-threads if you installed via some package management tools, I guess they would install this way by default. try: mdrun -t Thank you for your help James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Domain decomposition error in alchemical free energy perturbation MD
Hi everyone, With the help of one senior colleague, the problem has been solved. It turned out that if the parameter couple-moltype is turned on in the mdp, there will be always a warning of distant pair interaction which should not appear in the system. Once turned off, the warning disappears as well. It was my misunderstanding of the functions of these parameters involved (couple-moltype, couple-lambda0, couple-lambda1, etc) from the very beginning. For a solvation/binding free energy calculation, where the molecule is being decoupled from the system, it is more convenient to provide these parameters because it saves the efforts of putting parameters for state B in the topology. But in the case of alchemical FEP calculation, where only a few atoms of a residue are mutated, the decoupling of the whole molecule becomes unnecessary and problematic. The correct way is to implement the topology for both state A and state B, which removes the incorrect interactions and is more reasonable. Any insights are welcome. Thanks for your attention! Best regards, Xiaoxiao On Sat, Oct 15, 2011 at 2:11 PM, Xiaoxiao He xxia...@ust.hk wrote: Dear all, I'm doing an slow-growth alchemical free energy perturbation calculation of the formation of a disulfide bridge between two Cysteines with Gromacs. I've had tried different ways to combine the topology of both state A and state B, and finally settled with the most direct way -- to mutate the atoms that have different partial charges in the two states, and transform the two hydrogen atoms into dummy atoms. As suggested by Gromacs manual and some messages from the internet, I put explicitly the OPLS parameters for the bonds, pairs, angles and dihedrals changed from state A to state B, and the grompp didn't give a warning. But when I was testing the production simulation on two processors, there was a warning of fatal error in the log file: = Initializing Domain Decomposition on 2 nodes Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 3.774 nm, LJC Pairs NB, atoms 12 205 multi-body bonded interactions: 0.640 nm, Ryckaert-Bell., atoms 1013 417 Minimum cell size due to bonded interactions: 4.151 nm Using 0 separate PME nodes Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Optimizing the DD grid for 2 cells with a minimum initial size of 5.189 nm The maximum allowed number of cells is: X 0 Y 0 Z 0 --- Program mdrun, VERSION 4.5.4 Source code file: domdec.c, line: 6436 Fatal error: There is no domain decomposition for 2 nodes that is compatible with the given box and a minimum cell size of 5.18876 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors = The atoms indexed 12 and 205 are a CD1 in Leu1 and another CB in Ala12 respectively. I checked the topology and found no entries containing both these atoms. What's weird is that there's no way for these two atoms to have bonded interactions, but it says in the log that they have a two-body bonded interaction with a distance of 3.774 nm, which I cannot understand. Does anyone have an explanation what this could mean? Any suggestion is appreciated! Thanks in advance! Xiaoxiao He Oct. 15, 2011 Attached are the input parameters for the production md: = -Input Parameters: integrator = sd nsteps = 200 init_step= 0 ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 10 comm_mode= Linear nstlog = 100 nstxout = 10 nstvout = 10 nstfout = 10 nstcalcenergy= 10 nstenergy= 100 nstxtcout= 1000 init_t = 0 delta_t = 0.0005 xtcprec = 1000 nkx = 36 nky = 36 nkz = 36 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = TRUE ePBC = xyz bPeriodicMols= FALSE bContinuation= FALSE bShakeSOR= FALSE etc = No nsttcouple = -1 epc = Berendsen epctype = Isotropic
[gmx-users] Simulation of membrane protein
Dear Gromacs's users! I'd like to simulate some membrane proteins in their native environment. Recently I've found a good tutotial of the same simulation of the KALP peptide in DPPC membrane ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html ). Is there someone who have also tried to make thit tutorial ? First of all its very intresting for me the positioning of the protein in the membrane via specific perl script called infrategro. What values for the cutoff radius as well as measurements of the area per lipid are most adequate for different membrane proteins? Could you also tell me some alternative ways of full algorithm of the protein insertion in the membrane? Thanks, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of membrane protein
James Starlight wrote: Dear Gromacs's users! I'd like to simulate some membrane proteins in their native environment. Recently I've found a good tutotial of the same simulation of the KALP peptide in DPPC membrane (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html). Is there someone who have also tried to make thit tutorial ? Yes, per our server logs, several hundred people have :) First of all its very intresting for me the positioning of the protein in the membrane via specific perl script called infrategro. What values for the cutoff radius as well as measurements of the area per lipid are most adequate for different membrane proteins? The ones given in the tutorial work quite well. They are the defaults suggested by the developers of InflateGRO. Could you also tell me some alternative ways of full algorithm of the protein insertion in the membrane? Careful use of genbox (but will require significantly more equilibration as there will be large gaps), or g_membed. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] would trjcat correctly delete extra frames?
Yes. Tsjerk On Oct 15, 2011 7:21 PM, Yun Shi yunsh...@gmail.com wrote: Hi all, I am doing simulations on cluster piece by piece with -maxh and -noappend options of mdrun. However, one piece crushed way before approaching the max hours for unknown reasons. As a result, the part0004.trr file contains a couple of frames ahead of part0004.cpt file, since the most .cpt was only written about 5 or 10 minutes before the crush. So I plan to continue with the part0004.cpt file, and I expect the part0005.trr file I will get would have its initial 3 or 4 frames duplicated (only # steps and time) with the last 3 or 4 frames in part0004.trr file. And when I concatenate them together with trjcat, would the last 3 or 4 frames in part0004.trr file be automatically deleted? and only the initial 3 or 4 frames in part0005.trr be included in the resulting .trr file? Thanks for any suggestion! Yun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to calculate the normal of plane for Tryptophan or how to get the comparison matrix in g_rms
Have you thought about using the cross product. If you took the cross product of the unit vector in the direction of every atom starting from atom 1 then moved on to starting from atom 2 and so on you would have a set of vectors normal to every group of three atoms. If you then normalised them and defined one to be pointing upwards you could then ensure using dot products that they all pointed the same way, a condition like if a.b 0 b=-b would probably work you could then take the mean of the vectors. This should give an average normal vector to the plane of the molecule. If you’re going to be doing this a lot I would suggest removing the inherent double counting (r12=-r21). You could also think about weighting normal vectors in the averaging, for instance you could do it based on the sine of the angle between the vectors which generated them, or the mass of the atoms (H’s will more out of plane than carbons typically) Hope that’s helpful Richard On 15/10/2011 15:45, xiaodong huang xiaodonghuang2...@gmail.com wrote: I send this message yesterday, but I myself donot see this message, so, I send it again, very sorry for the spam. Dear gmxer's I am simulating a protein, want to calculate the normal of plane for Tryptophan residue amino acid in that protein. We need to take into account that, in simulation, atoms of TRP vibrate all the time, and they are not always on the same plane: If they were on the same plane in my simulation, to calculate the normal would be rather straighforward. As those atoms are not on the same plane, I think my calculation should be something like least square fitting. I look at g_rms command, and plan to calculate the normal in following steps: 1. create a Tryptophan with ideal configuration, where all 8 C atom and N atom (except CB atom) should be in the same plane, I put these 9 atoms in xy plane, and the normal of this TRP molecule is just z axis 2.I then calculate the rms between the TRP residue in my simulation and that ideal TRP molecule 3.If I know the rotate matrix (e.g. how to rotate the TRP in my simulation in the least-squares fitting of rms calculation), then I just rotate z axis (0,0,1) back ( in other words, multiple z axis (0,0,1) with the inverse of that rotate matrix) to get the plane normal for TRP in my simulation. So, I am wondering how to know the the rotate matrix when g_rms do the least-squares fitting? Is that in the comparison matrix dumped by the -bin option? If so, how to read the rotate matrix from that binary file produced by -bin option? Or, if there is other way that I can calculate plane normal for TRP? Thank you so much for your kind help. yours xiaodong school of chem, ANU -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to calculate the normal of plane for Tryptophan or how to get the comparison matrix in g_rms
On 16/10/2011 6:12 AM, Broadbent, Richard wrote: Have you thought about using the cross product. If you took the cross product of the unit vector in the direction of every atom starting from atom 1 then moved on to starting from atom 2 and so on you would have a set of vectors normal to every group of three atoms. If you then normalised them and defined one to be pointing upwards you could then ensure using dot products that they all pointed the same way, a condition like if a.b 0 b=-b would probably work you could then take the mean of the vectors. This should give an average normal vector to the plane of the molecule. If you're going to be doing this a lot I would suggest removing the inherent double counting (r12=-r21). You could also think about weighting normal vectors in the averaging, for instance you could do it based on the sine of the angle between the vectors which generated them, or the mass of the atoms (H's will more out of plane than carbons typically) Calculating the principle axes of inertia is a better approach. There's a GROMACS tool that does it. Mark Hope that's helpful Richard On 15/10/2011 15:45, xiaodong huang xiaodonghuang2...@gmail.com wrote: I send this message yesterday, but I myself donot see this message, so, I send it again, very sorry for the spam. Dear gmxer's I am simulating a protein, want to calculate the normal of plane for Tryptophan residue amino acid in that protein. We need to take into account that, in simulation, atoms of TRP vibrate all the time, and they are not always on the same plane: If they were on the same plane in my simulation, to calculate the normal would be rather straighforward. As those atoms are not on the same plane, I think my calculation should be something like least square fitting. I look at g_rms command, and plan to calculate the normal in following steps: 1. create a Tryptophan with ideal configuration, where all 8 C atom and N atom (except CB atom) should be in the same plane, I put these 9 atoms in xy plane, and the normal of this TRP molecule is just z axis 2.I then calculate the rms between the TRP residue in my simulation and that ideal TRP molecule 3.If I know the rotate matrix (e.g. how to rotate the TRP in my simulation in the least-squares fitting of rms calculation), then I just rotate z axis (0,0,1) back ( in other words, multiple z axis (0,0,1) with the inverse of that rotate matrix) to get the plane normal for TRP in my simulation. So, I am wondering how to know the the rotate matrix when g_rms do the least-squares fitting? Is that in the comparison matrix dumped by the -bin option? If so, how to read the rotate matrix from that binary file produced by -bin option? Or, if there is other way that I can calculate plane normal for TRP? Thank you so much for your kind help. yours xiaodong school of chem, ANU -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Normal Mode Analysis
On 16/10/2011 4:31 AM, James Starlight wrote: Thanks It's works fine but I'venot find significant increasing in the simulation speed :) If you've configured with threads, then executing mdrun will spawn as many threads as you have physical cores. This will speed up the calculation so long as it runs for more than a few seconds. but I'd also to test MPI. Could you tell me what exactly ( MPI or threading) might provide better productivity in case of big heterogenious system ( e.g protein in membrane )? It depends. MPI is required if your processors are not on the same piece of silicon, and is almost as good as threading if they are. Threading works if they are. Mark James 2011/10/15 lina lina.lastn...@gmail.com mailto:lina.lastn...@gmail.com On Sat, Oct 15, 2011 at 2:58 AM, James Starlight jmsstarli...@gmail.com mailto:jmsstarli...@gmail.com wrote: Dear Gromacs users! I have couple of questions about some Gromacs features. 1- I'm looking for tutorial where I could find clear example of force fied based Normal Mode Analysis via Gromacs E.g on first step I would like to prepare structure of my protein in pereodic boundary conditions and conduct energy minimization ( I've already can do it). Next I'd like to conduct full-atomic Normal Mode analysis and obtain motion trajectories along some lowest frequency modes for futher visualization in VMD. Finally I'd like to obtain information about frequencies ( eigenvalues) of each mode as well as frequencies of each residue fluctuations along different modes. 2- Also I'm looking for possible ways to enhanse Gromacs efficiency eg via ussage of multi cores of my CPU. I've found possible sillution via MPI function but this way dowsnt work in my case. How I can activate hyperthreading function as well as other possible ways ? If you installed from src, during configure --enable-threads if you installed via some package management tools, I guess they would install this way by default. try: mdrun -t Thank you for your help James -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] water passage during simulation
Hi GROMACS users, I have done simulation of a membrane protien named aquaporin5 which transports water across the membrane. I have done simulation of 3 ns and want to pass water molecules during simulation. Is it possible to do in GROMACS? I want to know how to do? please help. Madhumita Das -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] water passage during simulation
madhumita das wrote: Hi GROMACS users, I have done simulation of a membrane protien named aquaporin5 which transports water across the membrane. I have done simulation of 3 ns and want to pass water molecules during simulation. Is it possible to do in GROMACS? I want to know how to do? 3 ns is far too short of a timeframe to see this type of activity spontaneously. You may need tens or hundreds of ns. You can force water through the channel with the pull code, but I would suggest you refer to the literature to see what others have done; you are not the first to try to get water or small molecules to move through transport proteins. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
