Re: [gmx-users] a residue move in extremely large scale in MD
Dear Catch ya, I have watched the trajectory of the simulation. Besdies, I got the PDb file for the whole 10 ns MD every 500 ps. Then I compared all the PDB files generated, and it confirms that 1 specific residues moves in an extremely large space. Can you give me an explaination on it? Cheers, Acoot - Original Message - From: Dallas Warren To: Discussion list for GROMACS users Cc: Sent: Wednesday, 8 August 2012 8:58 AM Subject: RE: [gmx-users] a residue move in extremely large scale in MD What information has "told you" that you have large scale movement? Where did that information come from, how was it generated? Have you watch the trajectory of this simulation to see how the residue actually moves? Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Acoot Brett > Sent: Wednesday, 8 August 2012 8:30 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] a residue move in extremely large scale in MD > > Dear Marck, > > Will you please give me some suggestions on how to decide whether the > probelm is from periodic boundary conditions? > > Cheers, > > Acoot > > > - Original Message - > From: Mark Abraham > To: Discussion list for GROMACS users > Cc: > Sent: Monday, 6 August 2012 10:31 PM > Subject: Re: [gmx-users] a residue move in extremely large scale in MD > > On 6/08/2012 8:58 PM, Acoot Brett wrote: > > Dear All, > > > > I have a protein with about 400 amino acids. I have done a production > MD of it. I find in the 400 amino acids, there is 1 amino acids, during > the whole MD process, this residue moves in a extremely large scope in > comparison with all the other residues. > > Do you think this single residue with extremely large-scale movement > in the whole MD has important biological function, or has no biological > function? > > I'd start by proving that it was not a problem with periodic boundary > conditions! If real, movement may or may not be indicative of > functional significance - the question is impossible to answer out of > context. > > Mark > -- gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] Simulated annealing in implicit solvent
On 8/7/12 8:10 PM, Ольга Кононова wrote: Hello, I got a problem, trying to make preparation (in particular, heating from 0 to 300 K) of my system in implicit solvent (GBSA OBC model). For gradual heating I use simulated annealing (see mdp below) and sd integrator, which allows me do not use thermostat. I also set up gen_vel = yes and gen_temp = 0 (I am not sure, is it correct way or not). The problem appears: on the 0th step in output line temperature is ~305 K and it drops to ~8 K during 0.7 ps of simulation after that it starts to fluctuate around constant value (~ 10 K). At the beginning in output file there is line 'Initial temperature: 0 K', but started mdrun shows Sounds like a known issue: http://redmine.gromacs.org/issues/757 temperature 305 K. At the same time 'Current ref_t for group System' changes correctly step by step. I did try different parameters (turn on thermostat, turn off annealing, set gen_vel 0 or 300 K) - the same story. My guess is the problem with minimization. Algorithm "steepest descent" had convergent for 300 steps (in spite of very low emtol which I set up) and total potential energy dropped to constant minimum, I recompiled gromacs with double precision but minimization result was the same. Looks like my system (it's ~40 atoms) fell in some local minimum which gives me high initial temperature. What is wrong? Or it's proper behavior? Does it matter that I use cut-offs? Your results will be very inaccurate and your simulations unstable. I have found the only way to obtain a reliable trajectory using implicit solvent is to use the optimized all-vs-all kernels. Set: pbc = no rlist = 0 nstlist = 0 rvdw = 0 rcoulomb = 0 rgbradii = 0 Pertaining to the issue you described, are you running on GPU or CPU? If it's GPU, I find the same behavior - regardless of the target temperature, mdrun always reports a temperature 10 K higher than the target. I cannot determine if it is an output bug or a calculation bug. The behavior you describe is consistent with simulated annealing not working with implicit solvent (I don't know whether it should or not) and thus getting stuck at 0 K and thus reporting 10 K throughout the simulation. If you're running on CPU, ignore the previous paragraph ;) -Justin Here is mdp file: define = -DFLEXIBLE constraints = none integrator = sd dt = 0.001; 1fs nsteps = 30 ; 300 ps nstcomm = 1 nstxout = 1000 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog = 10 ; frequency to write energies to log file nstenergy = 100 ; frequency to write energies to edr file nstcalcenergy = 100 vdwtype = cut-off coulombtype = cut-off pbc = no table-extension = 20.0 nstlist = 100 ns_type = grid rlist = 1.0 rcoulomb = 1.1 rvdw = 1.1 comm-mode = angular comm-grps = system optimize_fft = yes ;heating annealing = single annealing_npoints = 2 annealing_time = 0 300 annealing_temp = 0 300 ld_seed = 8072012 ; V-rescale temperature coupling is on Tcoupl = no tau_t = 0.02 tc_grps = system ref_t = 0 ; Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp = 0 gen_seed = 8042012 ; Implicit solvent implicit_solvent = GBSA gb_algorithm = OBC; Still ; HCT ; OBC nstgbradii = 1 rgbradii = 1.0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent sa_algorithm = Ace-approximation sa_surface_tension = -1 I will be very appreciated for any help. - Olga Kononova -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Simulated annealing in implicit solvent
Hello, I got a problem, trying to make preparation (in particular, heating from 0 to 300 K) of my system in implicit solvent (GBSA OBC model). For gradual heating I use simulated annealing (see mdp below) and sd integrator, which allows me do not use thermostat. I also set up gen_vel = yes and gen_temp = 0 (I am not sure, is it correct way or not). The problem appears: on the 0th step in output line temperature is ~305 K and it drops to ~8 K during 0.7 ps of simulation after that it starts to fluctuate around constant value (~ 10 K). At the beginning in output file there is line 'Initial temperature: 0 K', but started mdrun shows temperature 305 K. At the same time 'Current ref_t for group System' changes correctly step by step. I did try different parameters (turn on thermostat, turn off annealing, set gen_vel 0 or 300 K) - the same story. My guess is the problem with minimization. Algorithm "steepest descent" had convergent for 300 steps (in spite of very low emtol which I set up) and total potential energy dropped to constant minimum, I recompiled gromacs with double precision but minimization result was the same. Looks like my system (it's ~40 atoms) fell in some local minimum which gives me high initial temperature. What is wrong? Or it's proper behavior? Does it matter that I use cut-offs? Here is mdp file: define = -DFLEXIBLE constraints = none integrator = sd dt = 0.001; 1fs nsteps = 30 ; 300 ps nstcomm = 1 nstxout = 1000 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog = 10 ; frequency to write energies to log file nstenergy = 100 ; frequency to write energies to edr file nstcalcenergy = 100 vdwtype = cut-off coulombtype = cut-off pbc = no table-extension = 20.0 nstlist = 100 ns_type = grid rlist = 1.0 rcoulomb = 1.1 rvdw = 1.1 comm-mode = angular comm-grps = system optimize_fft = yes ;heating annealing = single annealing_npoints = 2 annealing_time = 0 300 annealing_temp = 0 300 ld_seed = 8072012 ; V-rescale temperature coupling is on Tcoupl = no tau_t = 0.02 tc_grps = system ref_t = 0 ; Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp = 0 gen_seed = 8042012 ; Implicit solvent implicit_solvent = GBSA gb_algorithm = OBC; Still ; HCT ; OBC nstgbradii = 1 rgbradii = 1.0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent sa_algorithm = Ace-approximation sa_surface_tension = -1 I will be very appreciated for any help. - Olga Kononova -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)...
On 8/08/2012 3:17 AM, rama david wrote:
Hi Gromacs Friends,
I am trying to install gromacs 4.5.4 in parallel operating system fedora 17
I am using dell T 3500 precision , 6C.
I downloaded openmppi-1.6
Command line to install
./configure --prefix=/usr/local
make all install
For fftw 3.3.2 installation command line was .
./configure --enable-float
make
make install
To Gromacs I wrote..
./configure --enable-mpi --with-fft=fftw3 --program-suffix=_mpi
System reply with
configure error : cannot compute sizeof ( off_t)...
config .log show following error...It very big..I am pesting only a
small part...
Please tell me the reason for such error ...?? And how to overcome these???
I do not think your MPI compiler is working correctly. I suggest you
find a small test case to probe whether it is.
Mark
.
.
.
.
.
.
configure:5529: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.5.4"
| #define PACKAGE_STRING "gromacs 4.5.4"
| #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
| #define PACKAGE_URL ""
| #define PACKAGE "gromacs"
| #define VERSION "4.5.4"
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME "Tue Aug 7 10:46:37 IST 2012"
| #define BUILD_MACHINE "Linux 3.5.0-2.fc17.x86_64 x86_64"
| #define GMX_MPI /**/
| #define GMX_LIB_MPI /**/
| #define MPI_IN_PLACE_EXISTS /**/
| /* end confdefs.h. */
|
| #if defined __QK_USER__
| #else
| #error not catamount
| #endif
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:5551: result: no
configure:6229: checking how to run the C preprocessor
configure:6260: mpicc -E -I/usr/local/lib conftest.c
configure:6260: $? = 0
configure:6274: mpicc -E -I/usr/local/lib conftest.c
conftest.c:22:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:6274: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.5.4"
| #define PACKAGE_STRING "gromacs 4.5.4"
| #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
| #define PACKAGE_URL ""
| #define PACKAGE "gromacs"
| #define VERSION "4.5.4"
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME "Tue Aug 7 10:46:37 IST 2012"
| #define BUILD_USER "prashant@prashant"
| #define BUILD_MACHINE "Linux 3.5.0-2.fc17.x86_64 x86_64"
| #define GMX_MPI /**/
| #define GMX_LIB_MPI /**/
| #define MPI_IN_PLACE_EXISTS /**/
| #define F77_OR_C_FUNC(name,NAME) name
| #define F77_OR_C_FUNC_(name,NAME) name
| /* end confdefs.h. */
| #include
configure:6299: result: mpicc -E
configure:6319: mpicc -E -I/usr/local/lib conftest.c
configure:6319: $? = 0
configure:6333: mpicc -E -I/usr/local/lib conftest.c
conftest.c:22:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:6333: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.5.4"
| #define PACKAGE_STRING "gromacs 4.5.4"
| #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
| #define PACKAGE_URL ""
| #define PACKAGE "gromacs"
| #define VERSION "4.5.4"
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME "Tue Aug 7 10:46:37 IST 2012"
| #define BUILD_USER "prashant@prashant"
| #define BUILD_MACHINE "Linux 3.5.0-2.fc17.x86_64 x86_64"
| #define GMX_MPI /**/
| #define GMX_LIB_MPI /**/
| #define MPI_IN_PLACE_EXISTS /**/
| #define F77_OR_C_FUNC(name,NAME) name
| #define F77_OR_C_FUNC_(name,NAME) name
| /* end confdefs.h. */
| #include
configure:6362: checking for grep that handles long lines and -e
configure:6420: result: /usr/bin/grep
configure:6425: checking for egrep
configure:6487: result: /usr/bin/grep -E
configure:6492: checking whether ln -s works
configure:6496: result: yes
configure:6895: checking whether mpicc accepts -O3
configure:6913: result: yes
configure:7193: checking whether mpicc accepts -msse2
configure:7211: result: yes
configure:7225: checking whether mpicc accepts -funroll-all-loops
configure:7243: result: yes
configure:7255: checking whether mpicc accepts -std=gnu99
configure:7273: result: yes
configure:7288: checking whether mpicc accepts -fexcess-precision=fast
configure:7306: result: yes
configure:7347: checking whether mpicc accepts -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -fexcess-precision=fast
configure:7365: result: yes
configure:8089: checking whether byte ordering is bigendian
configure:8104: mpicc -c -O3 -fomit-frame-pointer -finline-functions
-Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99
-fexcess-precision=fast -I/usr/local/lib conftest.c >&5
conftest.c:23:9: error: unknown type name 'not'
conftest.c:23:15: error
RE: [gmx-users] a residue move in extremely large scale in MD
What information has "told you" that you have large scale movement? Where did that information come from, how was it generated? Have you watch the trajectory of this simulation to see how the residue actually moves? Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Acoot Brett > Sent: Wednesday, 8 August 2012 8:30 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] a residue move in extremely large scale in MD > > Dear Marck, > > Will you please give me some suggestions on how to decide whether the > probelm is from periodic boundary conditions? > > Cheers, > > Acoot > > > - Original Message - > From: Mark Abraham > To: Discussion list for GROMACS users > Cc: > Sent: Monday, 6 August 2012 10:31 PM > Subject: Re: [gmx-users] a residue move in extremely large scale in MD > > On 6/08/2012 8:58 PM, Acoot Brett wrote: > > Dear All, > > > > I have a protein with about 400 amino acids. I have done a production > MD of it. I find in the 400 amino acids, there is 1 amino acids, during > the whole MD process, this residue moves in a extremely large scope in > comparison with all the other residues. > > Do you think this single residue with extremely large-scale movement > in the whole MD has important biological function, or has no biological > function? > > I'd start by proving that it was not a problem with periodic boundary > conditions! If real, movement may or may not be indicative of > functional significance - the question is impossible to answer out of > context. > > Mark > -- gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 > * Only plain text messages are allowed! > * 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 * Only plain text messages are allowed! * 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] Hydroxyapatite MD odd behavior
Thank you Justing... We are working on your observations... We are sure that we will get back on this issue as soon as we figure out what we have done wrong... Best, On Mon, 06 Aug 2012 15:29:04 -0400, Justin Lemkul wrote > On 8/6/12 3:13 PM, Ramon Garduno wrote: > > On Mon, 06 Aug 2012 13:52:46 -0400, Justin Lemkul wrote > > > >> Please provide all the necessary files, including topologies and > >> modified force field files. I don't have time to make and double- > >> check all of these files and it's better to use exactly the same > >> files you've been trying to use. > >> > > > > Dear Justin, > > > > Thank you for your prompt response and willingness to help us... > > > > Since we do not have problems with the protein-water system, we decided to > > look closely to what happens with the slab during the NVT simulation. Thus, > > I > > have placed in http://www.fis.unam.mx/~ramon/CursoDF/HAP/ for download all > > the > > files we are using (at your request) to analyze the extrange behavior > > observed > > on the tetrahedral phosphate ion. > > > > Hopefuly your trained eyes can see what we can not... > > > > Immediately there is a problem. Your cutoff values in the .mdp > files (which are incorrect for Gromos96 53A6) are larger than the > size of the small system will permit, causing grompp to fail with a > fatal error. If you're overriding this error with -maxwarn, then > you're trying to simulate an unreasonable system since it violates > the minimum image convention. > > If you're working with other systems that are larger or different, > please provide those files instead. I've already had to make a > large number of corrections to these files (mostly in atom > naming/capitalization) to get grompp to even run, so parsing out > those errors is somewhat annoying. > > -Justin > > -- > > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 -- Open WebMail Project (http://openwebmail.org) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] a residue move in extremely large scale in MD
Dear Marck, Will you please give me some suggestions on how to decide whether the probelm is from periodic boundary conditions? Cheers, Acoot - Original Message - From: Mark Abraham To: Discussion list for GROMACS users Cc: Sent: Monday, 6 August 2012 10:31 PM Subject: Re: [gmx-users] a residue move in extremely large scale in MD On 6/08/2012 8:58 PM, Acoot Brett wrote: > Dear All, > > I have a protein with about 400 amino acids. I have done a production MD of > it. I find in the 400 amino acids, there is 1 amino acids, during the whole > MD process, this residue moves in a extremely large scope in comparison with > all the other residues. > Do you think this single residue with extremely large-scale movement in the > whole MD has important biological function, or has no biological function? I'd start by proving that it was not a problem with periodic boundary conditions! If real, movement may or may not be indicative of functional significance - the question is impossible to answer out of context. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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] About Shake and Lincs Algorithm
On 8/7/12 9:17 AM, vidhya sankar wrote: Dear Justin , Thank you for your Previous useful reply I Have used the Lincs Alogrithim for NPT Equlibration MD. But For Main MD I would like to use Shake Algorithim With Shake _tol = 0.1 with continuation = yes Is it Correct to use two algorithm for simulation of same system (NPT, longMD) To which extent Will it Affect the result (Free energy)? Because I am doing Free energy calculation Based on Essential Dynamics ? Is it possible I'm not prepared to predict such things. Whatever conditions you choose, equilibrate sufficiently before collecting data. Switching algorithms and immediately collecting data rarely, if ever, makes sense. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Gromacs configuration error....configure error : cannot compute sizeof ( off_t)...
Hi Gromacs Friends,
I am trying to install gromacs 4.5.4 in parallel operating system fedora 17
I am using dell T 3500 precision , 6C.
I downloaded openmppi-1.6
Command line to install
./configure --prefix=/usr/local
make all install
For fftw 3.3.2 installation command line was .
./configure --enable-float
make
make install
To Gromacs I wrote..
./configure --enable-mpi --with-fft=fftw3 --program-suffix=_mpi
System reply with
configure error : cannot compute sizeof ( off_t)...
config .log show following error...It very big..I am pesting only a
small part...
Please tell me the reason for such error ...?? And how to overcome these???
.
.
.
.
.
.
configure:5529: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.5.4"
| #define PACKAGE_STRING "gromacs 4.5.4"
| #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
| #define PACKAGE_URL ""
| #define PACKAGE "gromacs"
| #define VERSION "4.5.4"
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME "Tue Aug 7 10:46:37 IST 2012"
| #define BUILD_MACHINE "Linux 3.5.0-2.fc17.x86_64 x86_64"
| #define GMX_MPI /**/
| #define GMX_LIB_MPI /**/
| #define MPI_IN_PLACE_EXISTS /**/
| /* end confdefs.h. */
|
| #if defined __QK_USER__
| #else
| #error not catamount
| #endif
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:5551: result: no
configure:6229: checking how to run the C preprocessor
configure:6260: mpicc -E -I/usr/local/lib conftest.c
configure:6260: $? = 0
configure:6274: mpicc -E -I/usr/local/lib conftest.c
conftest.c:22:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:6274: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.5.4"
| #define PACKAGE_STRING "gromacs 4.5.4"
| #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
| #define PACKAGE_URL ""
| #define PACKAGE "gromacs"
| #define VERSION "4.5.4"
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME "Tue Aug 7 10:46:37 IST 2012"
| #define BUILD_USER "prashant@prashant"
| #define BUILD_MACHINE "Linux 3.5.0-2.fc17.x86_64 x86_64"
| #define GMX_MPI /**/
| #define GMX_LIB_MPI /**/
| #define MPI_IN_PLACE_EXISTS /**/
| #define F77_OR_C_FUNC(name,NAME) name
| #define F77_OR_C_FUNC_(name,NAME) name
| /* end confdefs.h. */
| #include
configure:6299: result: mpicc -E
configure:6319: mpicc -E -I/usr/local/lib conftest.c
configure:6319: $? = 0
configure:6333: mpicc -E -I/usr/local/lib conftest.c
conftest.c:22:28: fatal error: ac_nonexistent.h: No such file or directory
compilation terminated.
configure:6333: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.5.4"
| #define PACKAGE_STRING "gromacs 4.5.4"
| #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
| #define PACKAGE_URL ""
| #define PACKAGE "gromacs"
| #define VERSION "4.5.4"
| #define GMX_SOFTWARE_INVSQRT /**/
| #define GMX_QMMM_GAUSSIAN /**/
| #define GMX_QMMM_ORCA /**/
| #define BUILD_TIME "Tue Aug 7 10:46:37 IST 2012"
| #define BUILD_USER "prashant@prashant"
| #define BUILD_MACHINE "Linux 3.5.0-2.fc17.x86_64 x86_64"
| #define GMX_MPI /**/
| #define GMX_LIB_MPI /**/
| #define MPI_IN_PLACE_EXISTS /**/
| #define F77_OR_C_FUNC(name,NAME) name
| #define F77_OR_C_FUNC_(name,NAME) name
| /* end confdefs.h. */
| #include
configure:6362: checking for grep that handles long lines and -e
configure:6420: result: /usr/bin/grep
configure:6425: checking for egrep
configure:6487: result: /usr/bin/grep -E
configure:6492: checking whether ln -s works
configure:6496: result: yes
configure:6895: checking whether mpicc accepts -O3
configure:6913: result: yes
configure:7193: checking whether mpicc accepts -msse2
configure:7211: result: yes
configure:7225: checking whether mpicc accepts -funroll-all-loops
configure:7243: result: yes
configure:7255: checking whether mpicc accepts -std=gnu99
configure:7273: result: yes
configure:7288: checking whether mpicc accepts -fexcess-precision=fast
configure:7306: result: yes
configure:7347: checking whether mpicc accepts -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-funroll-all-loops -std=gnu99 -fexcess-precision=fast
configure:7365: result: yes
configure:8089: checking whether byte ordering is bigendian
configure:8104: mpicc -c -O3 -fomit-frame-pointer -finline-functions
-Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99
-fexcess-precision=fast -I/usr/local/lib conftest.c >&5
conftest.c:23:9: error: unknown type name 'not'
conftest.c:23:15: error: expected '=', ',', ';', 'asm' or
'__attribute__' before 'universal'
conftest.c:23:15: error: unknown type name 'universal'
configure:8104: $? = 1
configure: failed program
[gmx-users] About Shake and Lincs Algorithm
Dear Justin , Thank you for your Previous useful reply I Have used the Lincs Alogrithim for NPT Equlibration MD. But For Main MD I would like to use Shake Algorithim With Shake _tol = 0.1 with continuation = yes Is it Correct to use two algorithm for simulation of same system (NPT, longMD) To which extent Will it Affect the result (Free energy)? Because I am doing Free energy calculation Based on Essential Dynamics ? Is it possible Thanks In advance With Regards S.Vidhyasankar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] RE: tutorials for Coarse-Grained MD Simulation
On 8/7/12 6:51 AM, J Peterson wrote: Thank you so much for clearing my doubt. I have another doubt that how can I use g_fg2cg program in reverse transformation (RT) while this program is not an internal GROMACS program. The RT tutorial in MARTINI website says that one has to compile and source the files from rev_trans.tar.gz. How do I do this step.? Follow whatever instructions they provide for the installation. It's probably just a modified version of Gromacs with an additional tool, so the installation would be like any you would do for a normal Gromacs distribution. Make sure to set a proper installation path to avoid overwriting your existing Gromacs installation. These files are also tested with Gormacs 3.3.1 version, how do they work with recent versions of GROMACS? They don't. People have discussed this problem previously. In theory, you could probably re-create whatever necessary input files (.top, .tpr, etc) under version 3.3.1 and process any trajectories created with more modern versions. Version 3.3.1 is ancient and there have been hundreds of bug fixes and feature enhancements since it came out. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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: tutorials for Coarse-Grained MD Simulation
Thank you so much for clearing my doubt. I have another doubt that how can I use g_fg2cg program in reverse transformation (RT) while this program is not an internal GROMACS program. The RT tutorial in MARTINI website says that one has to compile and source the files from rev_trans.tar.gz. How do I do this step.? These files are also tested with Gormacs 3.3.1 version, how do they work with recent versions of GROMACS? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/tutorials-for-Coarse-Grained-MD-Simulation-tp467p492.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] .top file
On 8/7/12 5:33 AM, Shima Arasteh wrote: Dear gmx users, I need to check a line of angle section in .top file. It is written: 2 1 3 5 What does the numbers show? the atom numbers of .pdb file? How can I check this line? The first three are atom numbers within the corresponding [moleculetype]. The last number is the function type for the iteraction. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Error in ligand coordinate file
On 8/7/12 5:08 AM, sai nitin wrote: Hi all, Recently i performed protein ligand complex simulation my aim is to compute free energy values using g_lie..i came across that to perform g_lie analysis one should two 2 MD simulation one is protein ligand complex simulation (this is done ) used Charmm 27 FF second one is simulate ligand in water...which is the step i got stuck i know it is simple but couldnt get through first step it self preparing ligand coordinate file which i already have as follows i ran PDB2gmx to generate topol.top file but couldnt succeed.. ligand coordinate file is given below ATOM 1 N -13.006 -12.965 -0.251 1.00 0.00 N ATOM 2 C -13.386 -13.020 1.035 1.00 0.00 C ATOM 3 C1 -13.037 -14.131 1.869 1.00 0.00 C ATOM 4 C2 -12.284 -14.007 -0.761 1.00 0.00 C ATOM 5 N1 -11.897 -15.079 0.059 1.00 0.00 N ATOM 6 C3 -12.288 -15.172 1.391 1.00 0.00 C ATOM 7 N2 -13.547 -13.886 3.036 1.00 0.00 N ATOM 8 N3 -14.076 -12.193 1.759 1.00 0.00 N ATOM 9 C4 -14.163 -12.729 2.956 1.00 0.00 C ATOM 10 N4 -11.887 -13.919 -2.092 1.00 0.00 N ATOM 11 H -11.305 -15.802 -0.326 1.00 0.00 H ATOM 12 H1 -12.027 -12.978 -2.454 1.00 0.00 H ATOM 13 C5 -11.368 -14.845 -3.008 1.00 0.00 C ATOM 14 C6 -11.534 -14.731 -4.394 1.00 0.00 C ATOM 15 C7 -11.032 -15.710 -5.270 1.00 0.00 C ATOM 16 C8 -10.360 -16.822 -4.750 1.00 0.00 C ATOM 17 C9 -10.189 -16.950 -3.375 1.00 0.00 C ATOM 18 C10 -10.690 -15.970 -2.515 1.00 0.00 C ATOM 19 C11 -11.203 -15.559 -6.724 1.00 0.00 C ATOM 20 C12 -12.302 -15.958 -7.389 1.00 0.00 C ATOM 21 O -11.918 -16.240 2.152 1.00 0.00 O ATOM 22 H2 -11.168 -16.702 1.710 1.00 0.00 H ATOM 23 H3 -14.661 -12.289 3.746 1.00 0.00 H ATOM 24 H4 -12.034 -13.914 -4.779 1.00 0.00 H ATOM 25 H5 -9.992 -17.547 -5.386 1.00 0.00H ATOM 26 H6 -9.692 -17.769 -2.991 1.00 0.00H ATOM 27 H7 -10.559 -16.076 -1.497 1.00 0.00 H ATOM 28 H8 -10.438 -15.123 -7.263 1.00 0.00 H ATOM 29 H9 -13.084 -16.397 -6.878 1.00 0.00 H ATOM 30 H10 -12.364 -15.825 -8.411 1.00 0.00 H Running PDB2gmx gives error as follows Fatal error: Residue '-13.' not found in residue topology database Can any tell me what is wrong in my coordinate file It is formatted incorrectly. PDB format requires fixed spacing and correct content. The file shown above lacks a residue name column. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] .top file
Dear gmx users, I need to check a line of angle section in .top file. It is written: 2 1 3 5 What does the numbers show? the atom numbers of .pdb file? How can I check this line? Thanks for your help. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Error in ligand coordinate file
Hi all, Recently i performed protein ligand complex simulation my aim is to compute free energy values using g_lie..i came across that to perform g_lie analysis one should two 2 MD simulation one is protein ligand complex simulation (this is done ) used Charmm 27 FF second one is simulate ligand in water...which is the step i got stuck i know it is simple but couldnt get through first step it self preparing ligand coordinate file which i already have as follows i ran PDB2gmx to generate topol.top file but couldnt succeed.. ligand coordinate file is given below ATOM 1 N -13.006 -12.965 -0.251 1.00 0.00 N ATOM 2 C -13.386 -13.020 1.035 1.00 0.00 C ATOM 3 C1 -13.037 -14.131 1.869 1.00 0.00 C ATOM 4 C2 -12.284 -14.007 -0.761 1.00 0.00 C ATOM 5 N1 -11.897 -15.079 0.059 1.00 0.00 N ATOM 6 C3 -12.288 -15.172 1.391 1.00 0.00 C ATOM 7 N2 -13.547 -13.886 3.036 1.00 0.00 N ATOM 8 N3 -14.076 -12.193 1.759 1.00 0.00 N ATOM 9 C4 -14.163 -12.729 2.956 1.00 0.00 C ATOM 10 N4 -11.887 -13.919 -2.092 1.00 0.00 N ATOM 11 H -11.305 -15.802 -0.326 1.00 0.00 H ATOM 12 H1 -12.027 -12.978 -2.454 1.00 0.00 H ATOM 13 C5 -11.368 -14.845 -3.008 1.00 0.00 C ATOM 14 C6 -11.534 -14.731 -4.394 1.00 0.00 C ATOM 15 C7 -11.032 -15.710 -5.270 1.00 0.00 C ATOM 16 C8 -10.360 -16.822 -4.750 1.00 0.00 C ATOM 17 C9 -10.189 -16.950 -3.375 1.00 0.00 C ATOM 18 C10 -10.690 -15.970 -2.515 1.00 0.00 C ATOM 19 C11 -11.203 -15.559 -6.724 1.00 0.00 C ATOM 20 C12 -12.302 -15.958 -7.389 1.00 0.00 C ATOM 21 O -11.918 -16.240 2.152 1.00 0.00 O ATOM 22 H2 -11.168 -16.702 1.710 1.00 0.00 H ATOM 23 H3 -14.661 -12.289 3.746 1.00 0.00 H ATOM 24 H4 -12.034 -13.914 -4.779 1.00 0.00 H ATOM 25 H5 -9.992 -17.547 -5.386 1.00 0.00H ATOM 26 H6 -9.692 -17.769 -2.991 1.00 0.00H ATOM 27 H7 -10.559 -16.076 -1.497 1.00 0.00 H ATOM 28 H8 -10.438 -15.123 -7.263 1.00 0.00 H ATOM 29 H9 -13.084 -16.397 -6.878 1.00 0.00 H ATOM 30 H10 -12.364 -15.825 -8.411 1.00 0.00 H Running PDB2gmx gives error as follows Fatal error: Residue '-13.' not found in residue topology database Can any tell me what is wrong in my coordinate file Thanks. Nitin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] RE: tutorials for Coarse-Grained MD Simulation
Those tutorials show most important things (e.g. how to build topology for given system) in CG Martini ff using Gromacs. You do not have to merge anything. Commands are the same as for atomistic simulations http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html Jan From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of J Peterson [think_bey...@aol.com] Sent: Tuesday, August 07, 2012 5:47 AM To: gmx-users@gromacs.org Subject: [gmx-users] RE: tutorials for Coarse-Grained MD Simulation Dear Jan, Thanks for the link. The tutorials available here are very helpful start preparing the systems for simulation but would like to know how to merge the custom version of Gromacs for CG available in Martini web site with my existing Gromacs installation. Moreover how to make use of all the available Martini files and programs with the recent version of GROMACS that is version 4? Thanks, Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/tutorials-for-Coarse-Grained-MD-Simulation-tp467p486.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 * Only plain text messages are allowed! * 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
