Re: [gmx-users] gmx trjconv -center not working?
Hi Justin, "A cubic box is already as compact as it can be." That's true and I understand that :) it's just that I have faced similar issues with trjconv that Mala appears to be grappling with, and this combination has always resolves it for me. I don't know why. I can attach test files that show this behavior. Rajat On Fri, 8 Feb 2019, 5:27 pm Justin Lemkul > > On 2/8/19 5:17 AM, Rajat Desikan wrote: > > Hi Mala, > > Please combine -center with "-pbc mol -ur compact" and check. > > Compact unit cell representation is only useful for dodecahedral and > octahedral boxes. A cubic box is already as compact as it can be. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.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. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gmx trjconv -center not working?
Hi Mala, Please combine -center with "-pbc mol -ur compact" and check. Regards, Rajat -- Dr. Rajat Desikan Invictus Oncology, Delhi -- 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] Problems during installation
Hi Szilard,
Your advice was perfect: I've installed gromacs 2018_2 on my computer and
I'm currently testing some sample runs which have speeded up 20 times!
However, I consistently find that mdrun only selects one GPU when two are
available. Why does this happen?
*nvidia-smi*
Fri Jul 20 12:22:26 2018
+-+
| NVIDIA-SMI 396.24.10 Driver Version: 396.24.10
|
|---+--+--+
| GPU NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr.
ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute
M. |
|===+==+==|
| 0 GeForce GTX 108... Off | :01:00.0 Off |
N/A |
| 64% 60CP079W / 280W | 18MiB / 11176MiB | 0%
Default |
+---+--+--+
| 1 GeForce GTX 108... Off | :02:00.0 Off |
N/A |
| 0% 33CP8 9W / 280W | 2MiB / 11178MiB | 0%
Default |
+---+--+--+
*gmx_2018_2 mdrun -v -deffnm MD_test -nb gpu -gpu_id 01*
Using 1 MPI process
Using 12 OpenMP threads
1 GPU auto-selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
PP:0,PME:0
Regards,
Rajat
On Thu, Jul 19, 2018 at 8:40 PM Szilárd Páll wrote:
> On Mon, Jul 16, 2018 at 7:43 PM Rajat Desikan
> wrote:
>
> > Hi Mark,
> >
> > Thank you for the quick answer. My group is experimenting with a
> GPU-heavy
> > processor-light configuration similar to the Amber machines available
> from
> > Exxact (https://www.exxactcorp.com/AMBER-Certified-MD-Systems). In our
> > understanding, for this configuration to be successful performance-wise,
> > gromacs would've to do all the calculating on GPUs, and not just
> > electrostatics. That's why we're looking at openmm enabled versions.
> >
>
> For that you'd need the ~8 year old GROMACS 4.5 with OpenMM 2.x (IIRC)
> support which is ancient and unsupported so really not a good idea.
>
> Instead, use the latest release. Hardware-wise, ddeally you'd want to have
> 2-3 faster (wokstation) or 3-5 slower (server) cores per GPU for good
> CPU-GPU balance.
> --
> Szilárd
>
>
> > If you and others have alternate suggestions, we would be really eager to
> > hear them. Thank you for your time.
> >
> > Regards,
> > Rajat
> >
> > On Mon, 16 Jul 2018, 10:25 pm Mark Abraham,
> > wrote:
> >
> > > Hi,
> > >
> > > This code was not ever functional in the 4.6 branch, so if you want it
> to
> > > work, try 4.5.7. But really there is no reason to want to build it any
> > more
> > > - use the CUDA and OpenCL ports available in more recent GROMACS.
> > >
> > > Mark
> > >
> > > On Mon, Jul 16, 2018 at 6:47 PM Rajat Desikan
> > > wrote:
> > >
> > > > Dear all,
> > > > I'm trying to install openmm enabled version of gromacs 4.6.7 on a
> > 6-core
> > > > i7 machine with two GTX 1080 Ti GPUs. I am repeatedly facing a rather
> > > > strange error while running make:
> > > >
> > > > /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c: In function
> > > ‘cmain’:
> > > > /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: warning:
> > > > missing braces around initializer [-Wmissing-braces]
> > > >gmx_hw_opt_t hw_opt={0,0,0,0,TRUE,FALSE,0,NULL};
> > > >^
> > > > */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: note:
> > (near
> > > > initialization for ‘hw_opt’)*
> > > > */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:247:41: error:
> > > > ‘gmx_hw_opt_t {aka struct }’ has no member named ‘gpu_id’;
> > did
> > > > you mean ‘gpu_opt’?*
> > > > * { "-gpu_id", FALSE, etSTR, {_opt.gpu_id},*
> > > > ^
> > > > src/kernel/CMakeFiles/mdrun.dir/build.make:302: recipe for target
> > > > 'src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o' failed
> > > > make[2]: ***
> > > [src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o]
> > > > Error 1
> > > > CMakeFiles/Makefile2:1902: recipe for target
> > > > 'src/kernel/CMakeFiles/mdrun.dir/all' failed
> > > > make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2
> > > > Makefile:162: recipe for target 'all' failed
>
Re: [gmx-users] Problems during installation
Justin,
Lovely advice. I'll definitely consider it :) Thank you.
Regards,
Rajat
On Mon, Jul 16, 2018 at 11:15 PM Justin Lemkul wrote:
>
>
> On 7/16/18 1:42 PM, Rajat Desikan wrote:
> > Hi Mark,
> >
> > Thank you for the quick answer. My group is experimenting with a
> GPU-heavy
> > processor-light configuration similar to the Amber machines available
> from
> > Exxact (https://www.exxactcorp.com/AMBER-Certified-MD-Systems). In our
> > understanding, for this configuration to be successful performance-wise,
> > gromacs would've to do all the calculating on GPUs, and not just
> > electrostatics. That's why we're looking at openmm enabled versions.
> >
> > If you and others have alternate suggestions, we would be really eager to
> > hear them. Thank you for your time.
>
> IIRC, the OpenMM code in GROMACS only ever did implicit solvent
> calculations. With GROMACS 2018, all the nonbonded calculations are done
> on GPU with PME offload, which sounds exactly like what you want. You
> should be using a current version, not an ancient one :)
>
> -Justin
>
> > Regards,
> > Rajat
> >
> > On Mon, 16 Jul 2018, 10:25 pm Mark Abraham,
> > wrote:
> >
> >> Hi,
> >>
> >> This code was not ever functional in the 4.6 branch, so if you want it
> to
> >> work, try 4.5.7. But really there is no reason to want to build it any
> more
> >> - use the CUDA and OpenCL ports available in more recent GROMACS.
> >>
> >> Mark
> >>
> >> On Mon, Jul 16, 2018 at 6:47 PM Rajat Desikan
> >> wrote:
> >>
> >>> Dear all,
> >>> I'm trying to install openmm enabled version of gromacs 4.6.7 on a
> 6-core
> >>> i7 machine with two GTX 1080 Ti GPUs. I am repeatedly facing a rather
> >>> strange error while running make:
> >>>
> >>> /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c: In function
> >> ‘cmain’:
> >>> /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: warning:
> >>> missing braces around initializer [-Wmissing-braces]
> >>> gmx_hw_opt_t hw_opt={0,0,0,0,TRUE,FALSE,0,NULL};
> >>> ^
> >>> */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: note:
> (near
> >>> initialization for ‘hw_opt’)*
> >>> */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:247:41: error:
> >>> ‘gmx_hw_opt_t {aka struct }’ has no member named ‘gpu_id’;
> did
> >>> you mean ‘gpu_opt’?*
> >>> * { "-gpu_id", FALSE, etSTR, {_opt.gpu_id},*
> >>> ^
> >>> src/kernel/CMakeFiles/mdrun.dir/build.make:302: recipe for target
> >>> 'src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o' failed
> >>> make[2]: ***
> >> [src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o]
> >>> Error 1
> >>> CMakeFiles/Makefile2:1902: recipe for target
> >>> 'src/kernel/CMakeFiles/mdrun.dir/all' failed
> >>> make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2
> >>> Makefile:162: recipe for target 'all' failed
> >>> make: *** [all] Error 2
> >>>
> >>> I have installed cuda 9.1, openmm, fftw, open-mpi and all other
> necessary
> >>> software, so I'm at a loss. Please help me out. Google did not have
> much
> >>> leads.
> >>>
> >>> Thank you.
> >>>
> >>> Regards,
> >>> Rajat
> >>>
> >>> --
> >>> Dr. Rajat Desikan (Post Doctoral Fellow)
> >>> Prof. Narendra M Dixit's Lab (no 1),
> >>> Dept. of Chemical Engineering,
> >>> Indian Institute of Science, Bangalore
> >>> --
> >>> 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/Su
Re: [gmx-users] Problems during installation
Hi Mark,
Thank you for the quick answer. My group is experimenting with a GPU-heavy
processor-light configuration similar to the Amber machines available from
Exxact (https://www.exxactcorp.com/AMBER-Certified-MD-Systems). In our
understanding, for this configuration to be successful performance-wise,
gromacs would've to do all the calculating on GPUs, and not just
electrostatics. That's why we're looking at openmm enabled versions.
If you and others have alternate suggestions, we would be really eager to
hear them. Thank you for your time.
Regards,
Rajat
On Mon, 16 Jul 2018, 10:25 pm Mark Abraham,
wrote:
> Hi,
>
> This code was not ever functional in the 4.6 branch, so if you want it to
> work, try 4.5.7. But really there is no reason to want to build it any more
> - use the CUDA and OpenCL ports available in more recent GROMACS.
>
> Mark
>
> On Mon, Jul 16, 2018 at 6:47 PM Rajat Desikan
> wrote:
>
> > Dear all,
> > I'm trying to install openmm enabled version of gromacs 4.6.7 on a 6-core
> > i7 machine with two GTX 1080 Ti GPUs. I am repeatedly facing a rather
> > strange error while running make:
> >
> > /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c: In function
> ‘cmain’:
> > /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: warning:
> > missing braces around initializer [-Wmissing-braces]
> >gmx_hw_opt_t hw_opt={0,0,0,0,TRUE,FALSE,0,NULL};
> >^
> > */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: note: (near
> > initialization for ‘hw_opt’)*
> > */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:247:41: error:
> > ‘gmx_hw_opt_t {aka struct }’ has no member named ‘gpu_id’; did
> > you mean ‘gpu_opt’?*
> > * { "-gpu_id", FALSE, etSTR, {_opt.gpu_id},*
> > ^
> > src/kernel/CMakeFiles/mdrun.dir/build.make:302: recipe for target
> > 'src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o' failed
> > make[2]: ***
> [src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o]
> > Error 1
> > CMakeFiles/Makefile2:1902: recipe for target
> > 'src/kernel/CMakeFiles/mdrun.dir/all' failed
> > make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2
> > Makefile:162: recipe for target 'all' failed
> > make: *** [all] Error 2
> >
> > I have installed cuda 9.1, openmm, fftw, open-mpi and all other necessary
> > software, so I'm at a loss. Please help me out. Google did not have much
> > leads.
> >
> > Thank you.
> >
> > Regards,
> > Rajat
> >
> > --
> > Dr. Rajat Desikan (Post Doctoral Fellow)
> > Prof. Narendra M Dixit's Lab (no 1),
> > Dept. of Chemical Engineering,
> > Indian Institute of Science, Bangalore
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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mail to gmx-users-requ...@gromacs.org.
[gmx-users] Problems during installation
Dear all,
I'm trying to install openmm enabled version of gromacs 4.6.7 on a 6-core
i7 machine with two GTX 1080 Ti GPUs. I am repeatedly facing a rather
strange error while running make:
/home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c: In function ‘cmain’:
/home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: warning:
missing braces around initializer [-Wmissing-braces]
gmx_hw_opt_t hw_opt={0,0,0,0,TRUE,FALSE,0,NULL};
^
*/home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: note: (near
initialization for ‘hw_opt’)*
*/home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:247:41: error:
‘gmx_hw_opt_t {aka struct }’ has no member named ‘gpu_id’; did
you mean ‘gpu_opt’?*
* { "-gpu_id", FALSE, etSTR, {_opt.gpu_id},*
^
src/kernel/CMakeFiles/mdrun.dir/build.make:302: recipe for target
'src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o' failed
make[2]: *** [src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o]
Error 1
CMakeFiles/Makefile2:1902: recipe for target
'src/kernel/CMakeFiles/mdrun.dir/all' failed
make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2
Makefile:162: recipe for target 'all' failed
make: *** [all] Error 2
I have installed cuda 9.1, openmm, fftw, open-mpi and all other necessary
software, so I'm at a loss. Please help me out. Google did not have much
leads.
Thank you.
Regards,
Rajat
--
Dr. Rajat Desikan (Post Doctoral Fellow)
Prof. Narendra M Dixit's Lab (no 1),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
--
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
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Re: [gmx-users] Unable to install 5.1.14
Installing version 2016.3 worked perfectly. Thanks! Regards, Rajat On Mon, Aug 28, 2017 at 12:08 PM, Vytautas Rakeviius <vytautas1...@yahoo.com > wrote: > You have updated boost so you have to update GROMACS too. 2016.3 is the > latest version you should download it. > Another possibility is to downgrade boost to older, but you can bump into > other mish-mash issues. I do not recommend that. > > > > On Sunday, August 27, 2017, 11:36:21 PM GMT+3, Rajat Desikan < > rajatdesi...@gmail.com> wrote: > > Dear All, > I had removed gromacs 5.1.14. from my system (Ubuntu 16.04) a while ago, > and I'm having trouble reinstalling it. Cmake runs fine, but the system > repeatedly fails in the make step with this weird error: > > [ 3%] Building CXX object src/gromacs/CMakeFiles/ > libgromacs.dir/listed-forces/pairs.cpp.o > [ 3%] Building CXX object src/gromacs/CMakeFiles/ > libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o > In file included from /usr/local/include/boost/exception/detail/exception_ > ptr.hpp:20:0, > from /usr/local/include/boost/exception_ptr.hpp:9, > from /home/entropy/Downloads/gromacs-5.1.4/src/gromacs/ > utility/exceptions.h:53, > from /home/entropy/Downloads/gromacs-5.1.4/src/gromacs/ > commandline/cmdlineprogramcontext.cpp:62: > /usr/local/include/boost/exception/info.hpp: In member function ‘virtual > boost::shared_ptr > boost::exception_detail::error_info_container_impl::get(const > boost::exception_detail::type_info_&) const’: > /usr/local/include/boost/exception/info.hpp:102:28: error: use of deleted > function ‘boost::shared_ptr base>::shared_ptr(const > boost::shared_ptr&)’ > return p; > ^ > In file included from /usr/local/include/boost/shared_ptr.hpp:17:0, > from /home/entropy/Downloads/gromacs-5.1.4/src/gromacs/ > commandline/cmdlineprogramcontext.h:54, > from /home/entropy/Downloads/gromacs-5.1.4/src/gromacs/ > commandline/cmdlineprogramcontext.cpp:47: > /usr/local/include/boost/smart_ptr/shared_ptr.hpp:168:25: note: > ‘boost::shared_ptr base>::shared_ptr(const > boost::shared_ptr&)’ is > implicitly declared as deleted because ‘boost::shared_ptr exception_detail::error_info_base>’ declares a move constructor or move > assignment operator > > There are similar errors after this, and make fails. I have updated boost > on my system (version 58), and my system has the latest upgrades. Can > anyone please point out the way ahead? I've exhausted all easy options (Eg. > cleanly remove all gromacs associated files, redownload, untar and try to > install). > > My cmake command is: > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs514 -DGMX_USE_RDTSCP=off > > I've tried other permutations of the above command (without > -DGMX_USE_RDTSCP=off > for instance) and nothing seems to work. > > Thank you for your time. > > Regards, > Rajat > > -- > Dr. Rajat Desikan (Post Doctoral Fellow) > Prof. Narendra M Dixit's Lab (no 1), > Dept. of Chemical Engineering, > Indian Institute of Science, Bangalore > -- > 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. -- Dr. Rajat Desikan (Post Doctoral Fellow) Prof. Narendra M Dixit's Lab (no 1), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] SASA with rhombic dodecahedron
Dear All, SASA calculations of a solvated protein in a rhombic dodecahedron gives the following warning: WARNING: non-rectangular boxes may give erroneous results or crashes. Analysis based on vacuum simulations (with the possibility of evaporation) will certainly crash the analysis. Is there any way to go about this? Repeating the simulation is unfortunately not an option. Thanks. Regards, -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] SASA with rhombic dodecahedron
Thank you, Tsjerk. I will take a look. Are there any compatibility issues with a 4.6.4 trajectory and GMX 5 analysis tools? On Mon, Nov 10, 2014 at 4:04 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Rajat, Maybe try GMX 5. It appears this was fixed. Cheers, Tsjerk On Mon, Nov 10, 2014 at 9:49 AM, rajat desikan rajatdesi...@gmail.com wrote: Dear All, SASA calculations of a solvated protein in a rhombic dodecahedron gives the following warning: WARNING: non-rectangular boxes may give erroneous results or crashes. Analysis based on vacuum simulations (with the possibility of evaporation) will certainly crash the analysis. Is there any way to go about this? Repeating the simulation is unfortunately not an option. Thanks. Regards, -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] SASA with rhombic dodecahedron
Hi Tsjerk, Is this the resolved g_sas issue that you were alluding to? http://redmine.gromacs.org/issues/1445 I don't know if it is the solution to using a non-rectangular box. SASA calculations form an integral part of my conclusions, and I would like to be sure about their calculation. Thanks. Regards, On Mon, Nov 10, 2014 at 6:36 PM, rajat desikan rajatdesi...@gmail.com wrote: Thank you, Tsjerk. I will take a look. Are there any compatibility issues with a 4.6.4 trajectory and GMX 5 analysis tools? On Mon, Nov 10, 2014 at 4:04 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Rajat, Maybe try GMX 5. It appears this was fixed. Cheers, Tsjerk On Mon, Nov 10, 2014 at 9:49 AM, rajat desikan rajatdesi...@gmail.com wrote: Dear All, SASA calculations of a solvated protein in a rhombic dodecahedron gives the following warning: WARNING: non-rectangular boxes may give erroneous results or crashes. Analysis based on vacuum simulations (with the possibility of evaporation) will certainly crash the analysis. Is there any way to go about this? Repeating the simulation is unfortunately not an option. Thanks. Regards, -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Making index file
Hi, As an example, assuming that I have four chains (A,B,C,D) and want to select residue 14 in chains A,B and D 1 r 14 chain A|1 r 14 chain B| 1 r 14 chain D 1 is usually the default group 'protein'. If that is not so in your case, substitute it with the appropriate number. I think 3 is for CA atoms. I usually find that 1 r 14 Selects residue 14 in all chains in a multi chain protein. Hope that helps. Regards, On Wednesday, November 5, 2014, bharat gupta bharat.85.m...@gmail.com wrote: Hi, I want to make an index file for a certain residue, say residue 14 and its atom CA. I can eaily do that if its a single chain protein, but my protein contains 10 chains and I don't know how to select residue 14 from each chain. I tried splitting the protein into chains by using splitch option, but I don't know how proceed after that. Please help -- *Best Regards* Mn -- 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 javascript:;. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Making index file
Hi, If you are going to work with multiple chains, create a .tpr with a pdb file of your system that specifies the protein chains for analysis. Here is how I would do it. Take the initial .gro configuration of your MD run, convert it into pdb using editconf. Assign chain identifiers to the protein section and create an analysis.tpr using the same .top and .mdp as before. Use this .tpr to analyse your runs. Regards, On Wednesday, November 5, 2014, bharat gupta bharat.85.m...@gmail.com wrote: But is it necessary to renumber the residues .. Can this be done in some other way On Wed, Nov 5, 2014 at 2:49 PM, Eric Smoll ericsm...@gmail.com javascript:; wrote: [image: Boxbe] https://www.boxbe.com/overview This message is eligible for Automatic Cleanup! (ericsm...@gmail.com javascript:;) Add cleanup rule https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Ftoken%3DE9EnrGnFrM8VW1GJ8mZGxpbmcm1Z0OplUdfj9XjGPdGqU8a%252F570IPq%252BAkNHtIKRukk6ocJHWPiA7xqADmsV8TUZlZbrIkSR%252BK6gBYiEMND8ZA%252Fo%252BNJcq%252FyHnyimSjeY%252BPfnjhz2JLHI%253D%26key%3Dc15tC0ShNvPAlOoIApu2Dqp9oX4G1Rz8cfNqvpo6GQY%253Dtc_serial=19202815123tc_rand=163656utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 | More info http://blog.boxbe.com/general/boxbe-automatic-cleanup?tc_serial=19202815123tc_rand=163656utm_source=stfutm_medium=emailutm_campaign=ANNO_CLEANUP_ADDutm_content=001 Hello, Can you index your residues so that each residue gets a unique number. pdb2gmx has an option -renum that will do this for you. Best, Eric On Tue, Nov 4, 2014 at 10:33 PM, bharat gupta bharat.85.m...@gmail.com javascript:; wrote: Thank you for your response. But in the gro file there are no names for chains in mdrun.gro file. Moreover, if I am selecting only CA of residue 14 for chain A using the following command, I get 10 atoms, but I should get only 1 atom. r 14 a CA chain A. It means that the tool is taking CA of residue 14 from all 10 chains.. Still the problem remains unsolved On Wed, Nov 5, 2014 at 2:27 PM, rajat desikan rajatdesi...@gmail.com javascript:; wrote: Hi, As an example, assuming that I have four chains (A,B,C,D) and want to select residue 14 in chains A,B and D 1 r 14 chain A|1 r 14 chain B| 1 r 14 chain D 1 is usually the default group 'protein'. If that is not so in your case, substitute it with the appropriate number. I think 3 is for CA atoms. I usually find that 1 r 14 Selects residue 14 in all chains in a multi chain protein. Hope that helps. Regards, On Wednesday, November 5, 2014, bharat gupta bharat.85.m...@gmail.com javascript:; wrote: Hi, I want to make an index file for a certain residue, say residue 14 and its atom CA. I can eaily do that if its a single chain protein, but my protein contains 10 chains and I don't know how to select residue 14 from each chain. I tried splitting the protein into chains by using splitch option, but I don't know how proceed after that. Please help -- *Best Regards* Mn -- 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 javascript:; javascript:;. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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 javascript:;. -- 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 javascript:;. -- 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
Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle!
= pme_order= 6 optimize_fft = yes ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 30 ;** Also, I tried to relax my vesicle under NPT in vacuum in order to add water in a later step, but the NPT ended with a lot of LINCS warning (rotation more than 30 degrees). Okay, we read already that there are some information in the gmx-list discussing this problem, but the question is if it basically makes sense to follow the idea of a vaccum simulation or if we should directly start with solvated system in any case. Can you suggest us any method to solve this problem or maybe help us to improve our .mdp? Would be great! Best wishes, Manuel (and Björn) -- 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 javascript:;. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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 javascript:;. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Naughty Vacuum Bubble in our Vesicle
Dear Bjorn, A few thoughts: 1) Are you simulating a coarse grained system (Martini) or an all-atom system. Isotropic pressure coupling may be more appropriate for a vesicle because of its spherical symmetry. 2) When you manually added water, did you do it in the vacuum bubble region only? 3) What is that lateral tension in your vesicle? If your initial vesicle is tightly packed and has a lot of tension, it may expand to relax, in which case the internal density of the water may decrease in your production simulations. (see the PNAS paper from Marrink's group for the procedure to compute lateral tension). 4) Do you have sufficient water outside the vesicle to hydrate all the lipids in the outer leaflet? How about attaching a few snapshots so that we may take a look at them? Regards, On Tuesday, October 28, 2014, Björn Sommer bjo...@cellmicrocosmos.org wrote: Dear Andre, Rajat Stephane, thanks a lot for your light-speed suggestions! @More Water Idea I'll try to remove as less water as possible in my next try. But, what bothers me is the fact, that I manually added some water after the vacuum bubble was formed and equillibrated again, which resulted in another vaccuum bubble with the same or even larger size! From my understanding, this should not happen. Maybe I overlooked something? @Typo in MDP Thanks Stephane. We used a number of MDPs, we first have to check them all, if the typo was only an exception or if it was repeated several times. But we will take this into account but I fear, this is not causing the vacuum bubble - but we will check it! By the way, we are using GMX 4.6.X - would it make sense to switch to GMX 5? Thanks a lot best wishes! Manuel Björn -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Regarding msd
Hi, You need to use -pbc nojump to calculate the msd. Using -pbc whole is wrong for calculating the msd. On Tuesday, October 7, 2014, pratibha kapoor kapoorpratib...@gmail.com wrote: Hi all I have created my own code for msd calculation and would like to verify it from g_msd. I have created pdb files using trjconv -center -pbc whole option. Can I use the coordinates in pdb as such (with no wrapping/unwrapping/shifting) for running my code? or does the inbuild g_msd program modifies them (shift)? My msd values are not matching with the g_msd values. I suspect that discrepency in the pdb file creation since the values obtained from my program agrees with manual calculation (of some dummy values). Any suggestions are highly welcomed. -- 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 javascript:;. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Regarding msd
Hi Justin, I get identical results when I use g_msd (should have been clearer at the outset). However, if I extract the coordinates from an unprocessed trajectory with g_traj and run it in my own MSD code, I get different (and wrong) results than if I use -pbc nojump (which ensures a continuous trajectory). Since Pratibha wants to test her own code, the way she treats pbc is something to keep in mind. On Wed, Oct 8, 2014 at 4:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/8/14 3:21 AM, rajat desikan wrote: Hi, You need to use -pbc nojump to calculate the msd. Using -pbc whole is wrong for calculating the msd. Upon what do you base this statement? I get identical results with an unprocessed trajectory, and those treated with either -pbc whole or -pbc nojump. -Justin On Tuesday, October 7, 2014, pratibha kapoor kapoorpratib...@gmail.com wrote: Hi all I have created my own code for msd calculation and would like to verify it from g_msd. I have created pdb files using trjconv -center -pbc whole option. Can I use the coordinates in pdb as such (with no wrapping/unwrapping/shifting) for running my code? or does the inbuild g_msd program modifies them (shift)? My msd values are not matching with the g_msd values. I suspect that discrepency in the pdb file creation since the values obtained from my program agrees with manual calculation (of some dummy values). Any suggestions are highly welcomed. -- 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 javascript:;. -- == 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] adding ions in the genion for multimeric proteins
Hi, Use genion -neutral and let gromacs do that hard work. Regards, On Thu, Sep 4, 2014 at 9:03 AM, Ambarnil Ghosh ambargrom...@gmail.com wrote: Dear users, My protein is a trimer and I want to run md : on binding of a peptide (chain-D) to this trimer (chain-ABC). Therefore, I have four chains. So, when I create topol.top file using pdb2gmx it automatically divide the topology in four *.itp files: topol_Protein_chain_A.itp topol_Protein_chain_B.itp topol_Protein_chain_C.itp topol_Protein_chain_D.itp so, in time of running genion command its required to mention the number of ions to neutralize the protein. Now, each of the protein monomer contains net charge of 2 (qtot) in chain A, B and C. D-peptide have final qtot as 0. Now the question is : Where can I get final qtot for whole system? Is it like that: I have to just sum up all three (2+2+2) and write -nn 6 in genion command ? Or the final qtot value is written in somewhere else in some file, which I missed? I am new to multimeric simulation, any kind of help/lead is much appreciated! Thanks much Sincerely Nil -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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 to combine Slipid FF with amber FF?
Hi, Slipids are already compatible with Amber. Just download the proper lipid.itp file (DPPC.itp, DMPC.itp, ...) from the Slipids website, and include the below line in your .top after processing your protein with pdb2gmx (and selecting some Amber FF). ; Include lipid topology #include ./DMPC.itp Of course, you can change the name of the lipid.itp according to the lipids in your system. The order in which this appears in your .top matters. If you add the lipids to your simulation box and then solvate it, the above line must come prior to the water.itp Regards, On 8/31/14, Yorquant Wang wangy...@gmail.com wrote: Hi all, I want to do a membrane protein simulation and I want to use amber FF for protein (my target protein contains many beta sheet secondary structures). But forcefield.ff file in the web: http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html, contains only lipids parameter. I don't know how to conbined those lipid parameter with amber99sb-ildn.ff. Is there anybody who can help me? Thank you very much. -- Yukun Wang PhD candidate Institute of Natural Sciences College of Life Science, Shanghai Jiao Tong University Cell phone: 13621806236. China Shanghai -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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 to combine Slipid FF with amber FF?
Hi, I assumed that you had gone through the forcefield.ff files on Slipids webpage. You need to include the following section at the end in your ffnonbonded.itp (some of the spaces may be missing below). I suggest modifying a local copy of your desired Amber ff. ; SLIPIDS STARTS HERE HAL11 1.0080000.09A 0.235197261589 0.092048 HL 1 1.0080000.25A 0.12472582054 0.192464 HEL11 1.0080000.15A 0.2 0.10 ; New CL 6 12.011000.62A 0.356359487256 0.29288 CTL16 12.011000.14A 0.405358916754 0.08368 CTL36 12.0111-0.081 A 0.35000 0.3400 ; New CTL26 12.0011 0.05 A 0.35800 0.22800 ; New HAL31 1.00800 0.09 A 0.22000 0.09500 ; New HAL21 1.00800 0.09 A 0.24000 0.1120 ; New CTL56 12.01100-0.35 A 0.367050271874 0.33472 CEL16 12.01100-0.15 A 0.350.22 ; New CET16 12.01100-0.15 A 0.350.22 ; New, for trans double-bond OBL 8 15.999400 -0.52 A 0.302905564168 0.50208 OCL 8 15.999400 -0.76 A 0.302905564168 0.50208 O2L 8 15.999400 -0.78 A 0.302905564168 0.50208 OSL 8 15.999400 -0.49 A 0.293996576986 0.4184 ; Different to C27 OSLP8 15.999400 -0.57 A 0.293996576986 0.4184 ; Not in C27 NTL 7 14.00700-0.60 A 0.329632525712 0.8368 PL 15 30.974000 1.50A 0.38308644882.44764 HOL 1 1.0080000.43A 0.0400013524445 0.192464 OHL 8 15.999400 -0.66 A 0.315378146222 0.6363864 NH3L7 14.00700-0.30 A 0.329632525712 0.8368 HCL 1 1.0080000.33A 0.0400013524445 0.192464 CCL 6 12.011000.34A 0.356359487256 0.29288 HBL 1 1.0080000.10A 0.235197261589 0.092048 NH1 7 14.00700-0.47 A 0.329632525712 0.8368 H11 1 1.0080000.31A 0.0400013524445 0.192464 [ pairtypes ] ; 1-4 interactions ; i j funcsigma1-4epsilon1-4 CTL1CTL11 0.338541512893 0.04184 CTL1CTL21 0.338541512893 0.04184 CTL1CTL31 0.338541512893 0.04184 CTL1CTL51 0.338541512893 0.04184 CTL1OBL 1 0.293996576986 0.144938011577 CTL1HAL11 0.286869387241 0.06205874894 CTL1HAL21 0.288651184678 0.0700117110204 CTL1HAL31 0.288651184678 0.0648182492821 CTL1HL 1 0.231633666716 0.0897368027066 CTL1HEL11 0.280633096214 0.0736669217492 CTL1CEL11 0.355468588538 0.109105371453 CTL1CET11 0.355468588538 0.109105371453 CTL1OSL 1 0.316269044940 0.132309697301 CTL1OSLP1 0.316269044940 0.132309697301 CTL1NTL 1 0.334087019303 0.187114168357 CTL1PL 1 0.360813980846 0.320014464673 CTL1HOL 1 0.189271432669 0.0897368027066 CTL1OHL 1 0.326959829558 0.163176 ; CTL2CTL21 0.321 0.08184 ; New CTL2HAL21 0.268651184678 0.0200117110204 ; New CTL2CTL31 0.325 0.10184 ; New CTL3HAL21 0.278651184678 0.0200117110204 ; New CTL2CTL51 0.338541512893 0.04184 CTL2OBL 1 0.293996576986 0.144938011577 CTL2HAL11 0.286869387241 0.06205874894 CTL2HAL31 0.288651184678 0.0648182492821 CTL2HL 1 0.231633666716 0.0897368027066 CTL2HEL11 0.280633096214 0.0736669217492 CTL2CL 1 0.347450500074 0.110698234855 CTL2CEL11 0.355468588538 0.109105371453 CTL2CET11 0.355468588538 0.109105371453 CTL2OCL 1 0.320723538531 0.144938011577 CTL2O2L 1 0.320723538531 0.144938011577 CTL2OSL 1 0.316269044940 0.132309697301 CTL2OSLP1 0.316269044940 0.132309697301 CTL2NTL 1 0.334087019303 0.187114168357 CTL2PL 1 0.360813980846 0.320014464673 CTL2HOL 1 0.189271432669 0.0897368027066 CTL2OHL 1 0.326959829558 0.163176 CTL2HCL 1 0.189271432669 0.0897368027066 CTL2NH3L1 0.334087019303 0.187114168357 CTL2OCL 1 0.320723538531 0.144938011577 CTL2HCL 1 0.189271432669 0.0897368027066 ; CTL3CTL31 0.338541512893 0.04184 CTL3CTL51
Re: [gmx-users] gromacs
Hi, There is no problem in doing the simulation in parts as long as you take care to ensure continuity by using .cpt files, etc. You can concatenate the trajectory in the end for analysis. Regards, On 8/30/14, Meenakshi Rajput ashi.rajpu...@gmail.com wrote: hello users Can anyone tell me that is it necessary to run a long simulation at one tme? or I can do it in parts. Like if i am doing for 1000ps, can i do 500 at one tme and rest in next run? Would it give same results or its a wrong procedure? -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Plotting hydrogen bonds and salt bridges.
Hi Dawid, In my understanding, a hydrogen bond is considered between one set of hydrogen-donor-acceptor in Gromacs. So, when your water molecule flips and its oxygen becomes the acceptor, it is considered as a different hydrogen bond. So, the plot you have two hydrogen bonds each with differing lifetimes, one short and the other long. I think that g_hbond takes this into account. There are different ways to plot the salt-bridge distances. The criteria used by VMD makes sense to me. VMD defines a salt-bridge between two residues if *any* oxygen of the acidic residue (Asp, Glu) falls within the cut-off distance of *any* nitrogen of the basic residue (Arg, Lys, His). However, the salt bridge distance is computed between the center of mass of all the oxygen atoms in the acidic residue side chain and the center of mass of all the nitrogen atoms in the basic residue. This distance is different than the acceptance criteria for salt bridges (like you rightly recognized), but is necessary since residues like Arginine have multiple nitrogen atoms which can switch in the salt bridge formation due to thermal motion. Regards, On Sun, Aug 24, 2014 at 12:22 AM, Dawid das add...@googlemail.com wrote: Dear Gromacs experts, This time I have a question not regarding Gromacs itself but rather MD analysis in general. Let's say that I want to plot the distance between water and atom of an amino acid residue forming hydrogen bond. Now, how can I do it when water is donor of this h-bond and water molecule flips during the simulation so that the acutal donor changes? If you don't get me, have a look at this screenshot: http://www.speedyshare.com/8xHDs/Zrzut-ekranu-z-2014-08-23-19-33-45.png These two plots display distance between one residue atom and two different hydrogen atoms of the same water molecule. Now I think you understand what I mean. So, is it okay to leave it like this to show that there is constant h-bond between this water residue and amino acid residue? Or should I plot it differently? Now, I have similar question regarding salt bridges. Let's say there is salt bridge between one atom carrying negative charge and arginine residue. So how to plot distance between arginine side chain and this perticular atom? Which atom(s) of arginine should I take? Thank you, Dawid Grabarek -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] g_sas
Hi Eric,
1) Yes. Use a probe radius of 0 nm.
2) No. There is no verbose option in g_sas AFAIK. As an aside, you may want
to reconsider -xvg none
3) No difference in my experience.
4) g_sas uses vdwradii.dat, which may not have the vdw radius for a
particular atom type. Eg: Phosphorus is not present by default in
vdwradii.dat (for phosphorylated proteins). You may add this manually to a
local copy of vdwradii.dat
Regards,
On Sat, Aug 16, 2014 at 9:01 PM, Eric Smoll ericsm...@gmail.com wrote:
Hello,
I am interested in using g_sas in gromacs 4.6.5. I have a few questions:
1.) Is it advisable to use this tool to compute the vacuum accessible
surface area for a liquid?
2.) I ran a test using .gro / .trr / .tpr output from a production run in
my workflow as shown follows: { g_sas -f A.gro -s A.tpr -o TEST1.xvg -xvg
none -b 2000 -e 4000 -probe 0.15 -pbc -minarea 0.2 -ndots 24 -i TEST1.itp;
g_sas -f A.trr -s A.tpr -o TEST2.xvg -xvg none -b 2000 -e 4000 -probe 0.15
-pbc -minarea 0.2 -ndots 24 -i TEST2.itp }. The .trr / .tpr run produces no
output while processing so it is unclear when it will end. Is there anyway
to enable output that will report on the progress of the calculation?
3.) What are the difference in output when processing a .gro vs a .trr?
Does trajectory input produce trajectory output or some sort of average?
4.) When running on the .gro / .tpr combination I received the following
error:
WARNING: Masses and atomic (Van der Waals) radii will be guessed
based on residue and atom names, since they could not be
definitively assigned from the information in your input
files. These guessed numbers might deviate from the mass
and radius of the atom type. Please check the output
files if necessary.
WARNING: could not find a Van der Waals radius for 640 atoms
29440 out of 34560 atoms were classified as hydrophobic
Note that I am using 640 molecules in my liquid simulation. I have not
received this error for any other step in my molecular dynamics workflow.
It concerns me. Is this an indication that my coordinate and parameter
files are somehow incomplete? How do I go about troubleshooting this and
specifying the missing parameters?
Best,
Eric
--
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--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] g_sas
Hi Eric,
Sorry, I misread your mail. You cannot compute the vacuum accessible
surface area for a liquid because the molecules are in constant motion.
Regards,
On Sat, Aug 16, 2014 at 9:15 PM, rajat desikan rajatdesi...@gmail.com
wrote:
Hi Eric,
1) Yes. Use a probe radius of 0 nm.
2) No. There is no verbose option in g_sas AFAIK. As an aside, you may
want to reconsider -xvg none
3) No difference in my experience.
4) g_sas uses vdwradii.dat, which may not have the vdw radius for a
particular atom type. Eg: Phosphorus is not present by default in
vdwradii.dat (for phosphorylated proteins). You may add this manually to a
local copy of vdwradii.dat
Regards,
On Sat, Aug 16, 2014 at 9:01 PM, Eric Smoll ericsm...@gmail.com wrote:
Hello,
I am interested in using g_sas in gromacs 4.6.5. I have a few questions:
1.) Is it advisable to use this tool to compute the vacuum accessible
surface area for a liquid?
2.) I ran a test using .gro / .trr / .tpr output from a production run in
my workflow as shown follows: { g_sas -f A.gro -s A.tpr -o TEST1.xvg -xvg
none -b 2000 -e 4000 -probe 0.15 -pbc -minarea 0.2 -ndots 24 -i TEST1.itp;
g_sas -f A.trr -s A.tpr -o TEST2.xvg -xvg none -b 2000 -e 4000 -probe 0.15
-pbc -minarea 0.2 -ndots 24 -i TEST2.itp }. The .trr / .tpr run produces
no
output while processing so it is unclear when it will end. Is there anyway
to enable output that will report on the progress of the calculation?
3.) What are the difference in output when processing a .gro vs a .trr?
Does trajectory input produce trajectory output or some sort of average?
4.) When running on the .gro / .tpr combination I received the following
error:
WARNING: Masses and atomic (Van der Waals) radii will be guessed
based on residue and atom names, since they could not be
definitively assigned from the information in your input
files. These guessed numbers might deviate from the mass
and radius of the atom type. Please check the output
files if necessary.
WARNING: could not find a Van der Waals radius for 640 atoms
29440 out of 34560 atoms were classified as hydrophobic
Note that I am using 640 molecules in my liquid simulation. I have not
received this error for any other step in my molecular dynamics workflow.
It concerns me. Is this an indication that my coordinate and parameter
files are somehow incomplete? How do I go about troubleshooting this and
specifying the missing parameters?
Best,
Eric
--
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.
--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
--
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] g_sas
Hi Eric,
By vacuum accessible surface area, I assume that you mean the area defined
the surface of the interstitial volume. In my understanding, using g_sas
will give you the solvent accessible area (non buried area) averaged over
all the molecules and the trajectory. This is different from the
interstitial surface area. Someone please correct me if I am wrong.
Justin is correct when he says that the program displays time frames as it
analyses the trajectory. From your description, I feel that g_sas is stuck
on the first frame itself since it is calculating over all the liquid
molecules. And there is no way to figure out how much of that frame has
been analysed. What is your system made of?
I am not sure what you mean when you say trajectory like information. g_sas
prints out information for every time step.
Regards,
On Saturday, August 16, 2014, Justin Lemkul jalem...@vt.edu wrote:
On 8/16/14, 1:40 PM, Eric Smoll wrote:
Rajat,
Thank you for the rapid response. It is very helpful.
1) Yes. Use a probe radius of 0 nm.
2) No. There is no verbose option in g_sas AFAIK. As an aside, you may
want
to reconsider -xvg none
#2 is incorrect; all Gromacs programs print out which frame they are
working on to the terminal.
3) No difference in my experience.
Let me get this straight. You are saying that analyzing a .trr outputs an
average, not trajectory-like information. You are saying, for your
specific
system, you see little difference in the surface formed from analyzing a
trajectory and analyzing a snapshot. That may be for a protein but I am
studying a molecular liquid.
The type of output depends on what you ask for in your command line. The
use of -o will give you a time series of all the frames in your trajectory.
4) g_sas uses vdwradii.dat, which may not have the vdw radius for a
particular atom type. Eg: Phosphorus is not present by default in
vdwradii.dat (for phosphorylated proteins). You may add this manually to a
local copy of vdwradii.dat
Thank you. Exactly, the information I was looking for!
Sorry, I misread your mail. You cannot compute the vacuum accessible
surface area for a liquid because the molecules are in constant motion.
So are you saying that *I cannot use g_sas to compute the vacuum
accessible
surface area for a liquid at all* or *I cannot use g_sas to compute the
vacuum accessible surface area with a trajectory*?
Surely we can define a vacuum accessible surface for any timestep of this
trajectory, correct? I agree that molecules at the surface are constantly
changing making the definition of a surface ill-defined over a trajectory
but I am looking for some way to obtain a time-averaged atom-composition
of
the liquid surface. If g_sas can be used for temporal snaphot .gro file,
perhaps I can extract a variety of timesteps and carry out the calculation
manually.
This should not be necessary; you can provide the trajectory and g_sas
should do this for you. Whether or not that output is meaningful to you is
up to you; I have never dealt in vacuum-accessible SA.
-Justin
Thanks again Rajat,
Best,
Eric
Message: 7
Date: Sat, 16 Aug 2014 21:17:36 +0530
From: rajat desikan rajatdesi...@gmail.com
To: Discussion list for GROMACS users gmx-us...@gromacs.org
Subject: Re: [gmx-users] g_sas
Message-ID:
ca+d_lwtqq+0gphtq+8wqholrfqbwy6ycz6q-i4yag7hwmzh...@mail.gmail.com
Content-Type: text/plain; charset=UTF-8
Hi Eric,
Sorry, I misread your mail. You cannot compute the vacuum accessible
surface area for a liquid because the molecules are in constant motion.
Regards,
On Sat, Aug 16, 2014 at 9:15 PM, rajat desikan rajatdesi...@gmail.com
wrote:
Hi Eric,
1) Yes. Use a probe radius of 0 nm.
2) No. There is no verbose option in g_sas AFAIK. As an aside, you may
want to reconsider -xvg none
3) No difference in my experience.
4) g_sas uses vdwradii.dat, which may not have the vdw radius for a
particular atom type. Eg: Phosphorus is not present by default in
vdwradii.dat (for phosphorylated proteins). You may add this manually to
a
local copy of vdwradii.dat
Regards,
On Sat, Aug 16, 2014 at 9:01 PM, Eric Smoll ericsm...@gmail.com
wrote:
Hello,
I am interested in using g_sas in gromacs 4.6.5. I have a few
questions:
1.) Is it advisable to use this tool to compute the vacuum accessible
surface area for a liquid?
2.) I ran a test using .gro / .trr / .tpr output from a production run
in
my workflow as shown follows: { g_sas -f A.gro -s A.tpr -o TEST1.xvg
-xvg
none -b 2000 -e 4000 -probe 0.15 -pbc -minarea 0.2 -ndots 24 -i
TEST1.itp;
g_sas -f A.trr -s A.tpr -o TEST2.xvg -xvg none -b 2000 -e 4000 -probe
0.15
-pbc -minarea 0.2 -ndots 24 -i TEST2.itp }. The .trr / .tpr run produces
no
output while processing so it is unclear when it will end. Is there
anyway
to enable output that will report on the progress of the calculation?
3.) What are the difference in output when
Re: [gmx-users] Simulation at high temperature
Hi, You need to perform the NVT and NPT equilibration at 353.1 K and then use your equilibrated system for the production run. On Wed, Jul 16, 2014 at 10:55 AM, bharat gupta bharat.85.m...@gmail.com wrote: Hi, I first simulated my protein system at 300 K. Now I want to simulate the same protein system at high temperature (353.15 K). So, do I need to perform the npt and nvt equilibration again at 353.1 K first and then the final production run ?? Will it be okay to change the temp only in the production run file alone and continue the simulation ? Please respond Regards --- Bharat -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] pH simulation
Hi, http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation Gromacs users list: http://comments.gmane.org/gmane.science.biology.gromacs.user/40950 https://www.mail-archive.com/gmx-users@gromacs.org/msg05430.html On Thu, Jun 12, 2014 at 2:44 PM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi everyone... I want to do pH simulation in gromacs . I didn't found any specific link that I can follow for calculation regarding pH . Can you please guide me ..Any link that can help me... Thanks in advance Regards Lovika -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Problems with trajectories
Hi Steve, Did you try a plain -fit rot+trans in trjconv. That should remove both com translation as well as rotation. Select the 'protein' group for the least squares fit. On Tue, May 27, 2014 at 1:09 AM, Steve Seibold steve...@ymail.com wrote: I REALLY need some help here. I have tried for several days now and looked on line to fix the situation. My protein moves around and goes outside the simulation waterbox and my Zinc ions also frequently have bonds to protein of 40 angstroms are so. Here is one of the combinations I have tried so far to remove translational motion of protein and keep it in the center of the box: trajconv -f pr13.trr ( traj. file containing the last 8 ps) -s pr1.tpr (containing the first pdb structure before any MD, but with waters etc) -pbc atoms (place all atoms into center of box) -center -boxcenter tric -o protein13.trr This results in protein no longer separating into parts (pieces), but protein moves, still all over the box and outside of the box..and Zincs still have long bonds... Then, I use 'fit' as follows in an attempt to do a least squares fit of all trajectories (positions) back onto initial structure which is in center of box. trajconv -s pr1.tpr -f protein13.trr (using the output from above) -fit progressive -o protein13A.trr This didn't help at all.. I am really at a loss here on how to deal with this and could use some help.. Steve -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Citing gromacs tools
Thank you for the clarification, Prof. David. On Tuesday, May 13, 2014, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2014-05-13 07:52, rajat desikan wrote: Hi All, In many papers, the authors cite the main gromacs paper and simply declare in the methods section that they used the gromacs analysis suite. Is that a good practice or should each tool be cited separately? Eg: g_sas says: PLEASE READ AND CITE THE FOLLOWING REFERENCE Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael Scharf The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies J. Comp. Chem. 16 (1995) pp. 273-284 --- Thank You --- Thanks for asking. It is good practice to cite specific algorithms if they are available. In this particular case referees of your paper might (and should!) demand that as well. To make this easier gromacs tools print relevant references. You citing those papers also helps developers. -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Citing gromacs tools
Hi All, In many papers, the authors cite the main gromacs paper and simply declare in the methods section that they used the gromacs analysis suite. Is that a good practice or should each tool be cited separately? Eg: g_sas says: PLEASE READ AND CITE THE FOLLOWING REFERENCE Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael Scharf The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies J. Comp. Chem. 16 (1995) pp. 273-284 --- Thank You --- -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] vdw radii in g_sas
Thank you Justin, Tsjerk and Antonio for your detailed answers. g_sas computes uses the truncation distance for residue contacts by considering the minimum distance between residues. However, the papers I referred to has a Calpha-Calpha or Cbeta-Cbeta cutoff of 10-12 angstrom (default g_sas truncation criteria is 1.5 nm). Can anybody give heuristic suggestions about the truncation distance value? Thank you all for your time. On Sat, May 10, 2014 at 7:15 AM, Antonio Baptista bapti...@itqb.unl.ptwrote: You can indeed compute ff-dependent atomic radii from nonbonded parameters, which might be sometimes convenient (e.g., when trying to optimize a particular methodology). Some ways to do that are discussed in section 2.5 of http://dx.doi.org/10.1021/jp052259f. However, note that the surfaces, volumes, etc computed by tools like g_sas are physically vague properties. They are based on a geometrically well-defined but somewhat arbitrary algorithm (Lee-Richards, Connolly, etc), an idealized spherical solvent probe, and a vaguely defined set of atomic radii -- even if you use experimentally-derived van der Waals radii, their relation with the data (and thus their physical meaning) is neither straightforward nor unique. Since the properties that g_sas computes are physically vague, the important thing is to not depart too much from the usual methodology and allow others to reproduce your results. So, unless you are trying to do something unusual (as in the paper cited above), use the default GROMACS values and cite the version (which has a unique vdwradii.dat), or use instead a familiar set of radii (e.g., Bondi) and cite the corresponding paper. Cheers, Antonio On Fri, 9 May 2014, Tsjerk Wassenaar wrote: Do mind that the radius for P in PO4 is different from that for P alone. Cheers, Tsjerk On May 9, 2014 10:53 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/9/14, 3:35 PM, rajat desikan wrote: Thanks Justin. I am curious about the value for a phosphorus atom (protein in phospholipid bilayer; g_sas issues a warning). Do you know any reference for experimental values? Google knows. -Justin On Friday, May 9, 2014, Justin Lemkul jalem...@vt.edu wrote: On 5/9/14, 12:23 PM, rajat desikan wrote: Hi All, In the local copy of vdwradii.dat for g_sas calculations, the vdw radii are very approximate. Eg. C = 0.15 nm in vdwradii.dat, whereas ffnonbonded says sigma = 0.367 nm = vdwradius=0.185 nm Is it prudent to replace the values in the local vdwradii.dat with the vdwradii derived from ffnonbonded values? I would love to hear your thoughts/suggestions. No. The value of sigma will not give you the van der Waals radius of an atom. For each force field, the value is different, and it is based on optimized intermolecular distances. I don't think there's a clear way to turn this into some measure of an atom's size. If you're concerned that the values in vdwradii.dat are not sufficiently accurate, replace them with real experimentally determined values. -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. -- == 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
[gmx-users] vdw radii in g_sas
Hi All, In the local copy of vdwradii.dat for g_sas calculations, the vdw radii are very approximate. Eg. C = 0.15 nm in vdwradii.dat, whereas ffnonbonded says sigma = 0.367 nm = vdwradius=0.185 nm Is it prudent to replace the values in the local vdwradii.dat with the vdwradii derived from ffnonbonded values? I would love to hear your thoughts/suggestions. Thanks, -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Regarding the comparison of two result
Hi, I would suggest caution. I had a DPPC bilayer interacting with organic molecules (beta naphthol) which are supposed to alter the phase behaviour. The initial simulations using group cutoffs didn't capture one region of the experimental phase diagram, even with 200 ns of simulation (SLIPIDS + GAFF). However, I am able to capture this phase with Verlet cutoffs in version 4.6.4 in the high temperature range (Low temperature is problematic due to kinetic trapping in all simulations). This is probably because the Verlet cutoff scheme uses better model physics. So, make a cautious decision before going ahead. Regards, On Fri, May 2, 2014 at 5:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/2/14, 1:37 AM, rama david wrote: Dear Friends, I did MD simulation of two peptide that show that they form antiparallel beta sheet structure after 120 ns . i used gromacs 4.5.5 version. presently I completed MD simulation of another peptide ( Different sequence). but I am using gromacs 4.6.3 . I found that two peptide start to form anti parallelstructure around 15 ns. My question is that are this two result at all comparable as the version of software is diff. ?? is this result upto publication ??? I am looking forward for answer . I know this is a very simple but complicated to me. You'd have to look into the release notes to see if there were any relevant changes based on your run settings and such. There were hundreds of changes between 4.5.5 and 4.6.3 - changing between release series can be a bit dicey. Changes within a release series should give consistent results, except in the case of critical bugs being fixed (i.e. everything in 4.5.x should match, everything in 4.6.x should match, but 4.5.x and 4.6.x may not necessarily be the same, depending on what the relevant changes were). I would expect standard MD to probably be OK, but you really do need to look at all of the changes to determine if that's right. Rule of thumb (at least, in my mind) - pick a version (the newest one available at the time, or whatever makes sense for scientific continuity with other ongoing or completed work) and stick with it. -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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Regarding the comparison of two result
I forgot to mention that the earlier simulations were with version 4.5.4 On Fri, May 2, 2014 at 6:13 PM, rajat desikan rajatdesi...@gmail.comwrote: Hi, I would suggest caution. I had a DPPC bilayer interacting with organic molecules (beta naphthol) which are supposed to alter the phase behaviour. The initial simulations using group cutoffs didn't capture one region of the experimental phase diagram, even with 200 ns of simulation (SLIPIDS + GAFF). However, I am able to capture this phase with Verlet cutoffs in version 4.6.4 in the high temperature range (Low temperature is problematic due to kinetic trapping in all simulations). This is probably because the Verlet cutoff scheme uses better model physics. So, make a cautious decision before going ahead. Regards, On Fri, May 2, 2014 at 5:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/2/14, 1:37 AM, rama david wrote: Dear Friends, I did MD simulation of two peptide that show that they form antiparallel beta sheet structure after 120 ns . i used gromacs 4.5.5 version. presently I completed MD simulation of another peptide ( Different sequence). but I am using gromacs 4.6.3 . I found that two peptide start to form anti parallelstructure around 15 ns. My question is that are this two result at all comparable as the version of software is diff. ?? is this result upto publication ??? I am looking forward for answer . I know this is a very simple but complicated to me. You'd have to look into the release notes to see if there were any relevant changes based on your run settings and such. There were hundreds of changes between 4.5.5 and 4.6.3 - changing between release series can be a bit dicey. Changes within a release series should give consistent results, except in the case of critical bugs being fixed (i.e. everything in 4.5.x should match, everything in 4.6.x should match, but 4.5.x and 4.6.x may not necessarily be the same, depending on what the relevant changes were). I would expect standard MD to probably be OK, but you really do need to look at all of the changes to determine if that's right. Rule of thumb (at least, in my mind) - pick a version (the newest one available at the time, or whatever makes sense for scientific continuity with other ongoing or completed work) and stick with it. -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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] g_potential help
Hi All, I have a membrane-protein-solvent system, and I want the potential across the membrane in the direction of the membrane normal. I have 2 questions in that regard. 1) We know that epsilon_r = 80 for the water, ~7 for the membrane-water interface and ~2 for the hydrophobic membrane core. g_potential returns the result for epsilon_r = 1. How can I incorporate this into the result? 2) Default ng =1? Is the number of groups referring to the number of charge groups defined in the topology? Thank you for your time. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] g_potential help
Hi Justin, So different parts of my system in Z-direction should be scaled differently, right? On a coarse level, aqueous part with a scaling of 80, membrane with a scaling of 2? How do I correct for this? Can I take the quantitative output for potential difference across a membrane in water from g_potential literally? Thanks, On Monday, April 21, 2014, Justin Lemkul jalem...@vt.edu wrote: On 4/21/14, 9:58 AM, rajat desikan wrote: Hi All, I have a membrane-protein-solvent system, and I want the potential across the membrane in the direction of the membrane normal. I have 2 questions in that regard. 1) We know that epsilon_r = 80 for the water, ~7 for the membrane-water interface and ~2 for the hydrophobic membrane core. g_potential returns the result for epsilon_r = 1. How can I incorporate this into the result? I'd venture a guess that the value of epsilon_r in the output is the same as the interpretation of epsilon_r in the .mdp file - it is the relative dielectric permittivity. A value of 1 means don't scale anything; see previous discussions. 2) Default ng =1? Is the number of groups referring to the number of charge groups defined in the topology? No, that means the number of groups you want to analyze, just like g_rdf and other tools sometimes give the option of doing multiple analyses at the same time. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] strange do_dssp error
Update for anyone interested: Installing dssp 2.2.1 solved the above error! I am not sure why... On Sun, Feb 9, 2014 at 11:39 AM, rajat desikan rajatdesi...@gmail.comwrote: Hi All, I get this error while running do_dssp. The program reads the whole trajectory but fails to write a scount file. gmxcheck on the trajectory shows no problems. Any suggestions? (P.S. do_dssp worked fine on another simulation trajectory of similar size. To make sure that this was not a memory related issue, I ran this on my cluster too. Same fault.) Selected 36: 'HelixA' There are 324 residues in your selected group dssp cmd='/home/rajatdesikan/Desktop/dssp-2.0.4-linux-i386 -i ddT5iGbw -o ddOpjxP3 /dev/null 2 /dev/null' Reading frame 0 time0.000 Back Off! I just backed up ddT5iGbw to ./#ddT5iGbw.1# Reading frame 2 time 10.000 Back Off! I just backed up SS/protmem_ss_A.xpm to SS/#protmem_ss_A.xpm.1# 100% Back Off! I just backed up SS/protmem_ssdump_A.dat to SS/#protmem_ssdump_A.dat.1# *** glibc detected *** do_dssp: double free or corruption (!prev): 0x029ad9c0 *** === Backtrace: = /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7f68b0a8db96] do_dssp(gmx_do_dssp+0x3146)[0x41d5d6] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f68b0a3076d] do_dssp[0x419111] === Memory map: 0040-00877000 r-xp 08:06 6352669 /opt/apps/gromacs/4.6.3/gnu/serial/bin/do_dssp 00a76000-00a77000 r--p 00476000 08:06 6352669 /opt/apps/gromacs/4.6.3/gnu/serial/bin/do_dssp 00a77000-00a88000 rw-p 00477000 08:06 6352669 /opt/apps/gromacs/4.6.3/gnu/serial/bin/do_dssp 00a88000-00a89000 rw-p 00:00 0 023b5000-0365e000 rw-p 00:00 0 [heap] 7f68aec2-7f68aec35000 r-xp 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f68aec35000-7f68aee34000 ---p 00015000 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f68aee34000-7f68aee35000 r--p 00014000 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f68aee35000-7f68aee36000 rw-p 00015000 08:06 3014802 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f68aee36000-7f68afbf rw-p 00:00 0 7f68afce4000-7f68b0807000 rw-p 00:00 0 7f68b0807000-7f68b080e000 r-xp 08:06 3014971 /lib/x86_64-linux-gnu/librt-2.15.so 7f68b080e000-7f68b0a0d000 ---p 7000 08:06 3014971 /lib/x86_64-linux-gnu/librt-2.15.so 7f68b0a0d000-7f68b0a0e000 r--p 6000 08:06 3014971 /lib/x86_64-linux-gnu/librt-2.15.so 7f68b0a0e000-7f68b0a0f000 rw-p 7000 08:06 3014971 /lib/x86_64-linux-gnu/librt-2.15.so 7f68b0a0f000-7f68b0bc4000 r-xp 08:06 3014963 /lib/x86_64-linux-gnu/libc-2.15.so 7f68b0bc4000-7f68b0dc4000 ---p 001b5000 08:06 3014963 /lib/x86_64-linux-gnu/libc-2.15.so 7f68b0dc4000-7f68b0dc8000 r--p 001b5000 08:06 3014963 /lib/x86_64-linux-gnu/libc-2.15.so 7f68b0dc8000-7f68b0dca000 rw-p 001b9000 08:06 3014963 /lib/x86_64-linux-gnu/libc-2.15.so 7f68b0dca000-7f68b0dcf000 rw-p 00:00 0 7f68b0dcf000-7f68bG0ddc000 r-xp 08:06 4064338 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 7f68b0ddc000-7f68b0fdb000 ---p d000 08:06 4064338 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 7f68b0fdb000-7f68b0fdc000 r--p c000 08:06 4064338 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 7f68b0fdc000-7f68b0fdd000 rw-p d000 08:06 4064338 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 7f68b0fdd000-7f68b0ff5000 r-xp 08:06 3014974 /lib/x86_64-linux-gnu/libpthread-2.15.so 7f68b0ff5000-7f68b11f4000 ---p 00018000 08:06 3014974 /lib/x86_64-linux-gnu/libpthread-2.15.so 7f68b11f4000-7f68b11f5000 r--p 00017000 08:06 3014974 /lib/x86_64-linux-gnu/libpthread-2.15.so 7f68b11f5000-7f68b11f6000 rw-p 00018000 08:06 3014974 /lib/x86_64-linux-gnu/libpthread-2.15.so 7f68b11f6000-7f68b11fa000 rw-p 00:00 0 7f68b11fa000-7f68b12f5000 r-xp 08:06 3014978 /lib/x86_64-linux-gnu/libm-2.15.so 7f68b12f5000-7f68b14f4000 ---p 000fb000 08:06 3014978 /lib/x86_64-linux-gnu/libm-2.15.so 7f68b14f4000-7f68b14f5000 r--p 000fa000 08:06 3014978 /lib/x86_64-linux-gnu/libm-2.15.so 7f68b14f5000-7f68b14f6000 rw-p 000fb000 08:06 3014978 /lib/x86_64-linux-gnu/libm-2.15.so 7f68b14f6000-7f68b1518000 r-xp 08:06 3014980 /lib/x86_64-linux-gnu/ld-2.15.so 7f68b151b000-7f68b155 rw-p 00:00 0 7f68b1624000-7f68b16f5000 rw-p 00:00 0 7f68b1712000-7f68b1718000 rw-p 00:00 0 7f68b1718000-7f68b1719000 r--p 00022000 08:06 3014980 /lib/x86_64-linux-gnu/ld-2.15.so 7f68b1719000-7f68b171b000 rw-p 00023000 08:06 3014980 /lib/x86_64-linux-gnu/ld-2.15.so 7fff6c5e2000-7fff6c603000 rw-p 00:00 0 [stack] 7fff6c657000-7fff6c658000 r-xp 00:00 0 [vdso] ff60-ff601000 r-xp 00:00 0 [vsyscall] Aborted (core dumped) -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Rajat Desikan (Ph.D Scholar) Prof. K
Re: [gmx-users] g_helixorient help
Thanks for the super detailed reply, Bipin. I will try this out! On Fri, Jan 31, 2014 at 3:04 PM, bipin singh bipinel...@gmail.com wrote: Inter helical angle using *g_bundle * # 1. Do in make_ndx: # make_ndxGenerate indexes describing extremities of # the two helices. Select the CA of residues belonging #the extremities of each helix. make_ndx -f NAME.gro -o NAME_CROSSANGLE.ndx # Define other groups you need # Define 4 groups corresponding to the ends of the two helices # ... # q # 2. Do in a text editor: # Merge the 4 index groups, corresponding to helices ends, in order to get # two index groups, each containing either the beginning of the two # helices or the ends of the two helices. See g_bundle's online help. # The number of residues selected for each helix has to be the same. # 3. Do in g_bundle: # g_bundleGet coordinate of vectors describing the helices echo 0 1 | g_bundle -f NAME.xtc -s NAME.tpr -n NAME_CROSSANGLE.ndx \ -dt XX -b -e -na 2 -oa NAME_CROSSANGLE.pdb\ g_bundle.CROSSANGLE.out # -na 2; there are two axes this time # -oa NAME_CROSSANGLE.pdb ; to get the coordinates of the axes and check the angles given by the software # rm, Remove some unuseful files genererated by g_bundle: rm bun_len.xvg bun_dist.xvg bun_z.xvg bun_tilt.vxg bun_tiltl.xvg bun_tiltr.xvg # The first time, it might be helpful to open NAME_CROSSANGLE.pdb in rasmol or # vmd to visualize the data you are handling and check wether you define your # index correctly... and also two understand the structures of the data you # are handling. # The next part is dirty and could be automated with a smart script: # 4. Do in g_ traj # g_traj transform the .pdb trajectory in a file format easier to handle, # i.e a .xvg file. echo 0 | g_traj -f NAME_CROSSANGLE.pdb -s NAME_CROSSANGLE.pdb \ -ox NAME_CROSSANGLE.xvg g_traj.CROSSANGLE.out #In the header of the .xvg file, you have this: # @ legend string 0 atom 1 X # @ legend string 1 atom 1 Y # @ legend string 2 atom 1 Z # @ legend string 3 atom 2 X # @ legend string 4 atom 2 Y # @ legend string 5 atom 2 Z # @ legend string 6 atom 3 X # @ legend string 7 atom 3 Y # @ legend string 8 atom 3 Z # @ legend string 9 atom 4 X # @ legend string 10 atom 4 Y # @ legend string 11 atom 4 Z # @ legend string 12 atom 5 X # @ legend string 13 atom 5 Y # @ legend string 14 atom 5 Z # @ legend string 15 atom 6 X # @ legend string 16 atom 6 Y # @ legend string 17 atom 6 Z # 01.35431.23062.11210.85610.8589... # 201.40021.06922.04280.89430.7557... # 401.3591.07932.13410.86860.7528... # ...... # 5. Do in Microsoft Excel or equivalent # Import the .xvg file. You'll get a 19-column file. The first column # correspond to the time. The next 9 columns are (x,y,z) coordinates of 3 # points belonging to the vector describing the first helix and the next 9 # are coordinate of 3 points belonging to the second helix. # When this point is reached, you can define the vectors describing the # helices (by substracting coordinate of atom 3 and 1 and atom 6 and 4), # normalize them (by dividing the vector by their norm) and calulate their # dot-product in excel. # The dot product of two normalized vectors is the cosine of their # cross-angle. Disclaimer: Copied from an old gromacs discussion. On Thu, Jan 30, 2014 at 2:06 PM, rajat desikan rajatdesi...@gmail.com wrote: Hi All, Any suggestions? Thanks. On Mon, Jan 27, 2014 at 5:01 PM, rajat desikan rajatdesi...@gmail.com wrote: Hi All, I am trying to calculate the angle between the axes of two alpha helices (say A and B) in my simulation. I have separate index files for the residues pertaining to each helix. I calculated the tilt.xvg for both A and B. The output is slightly confusing. tilt_A.xvg when viewed with xmgrace -nxy shows 27 data sets. What do these correspond to? (Helix A has 34 residues). Similarly for bending_A.xvg How do I go about this? Is this the right way to calculate the relative helix axis angle? Thanks, -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] g_helixorient help
Hi All, Any suggestions? Thanks. On Mon, Jan 27, 2014 at 5:01 PM, rajat desikan rajatdesi...@gmail.comwrote: Hi All, I am trying to calculate the angle between the axes of two alpha helices (say A and B) in my simulation. I have separate index files for the residues pertaining to each helix. I calculated the tilt.xvg for both A and B. The output is slightly confusing. tilt_A.xvg when viewed with xmgrace -nxy shows 27 data sets. What do these correspond to? (Helix A has 34 residues). Similarly for bending_A.xvg How do I go about this? Is this the right way to calculate the relative helix axis angle? Thanks, -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] g_helixorient help
Hi All, I am trying to calculate the angle between the axes of two alpha helices (say A and B) in my simulation. I have separate index files for the residues pertaining to each helix. I calculated the tilt.xvg for both A and B. The output is slightly confusing. tilt_A.xvg when viewed with xmgrace -nxy shows 27 data sets. What do these correspond to? (Helix A has 34 residues). Similarly for bending_A.xvg How do I go about this? Is this the right way to calculate the relative helix axis angle? Thanks, -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] LR electrostatics in single point energy calculations
Hi Justin, I used the following commands: mdrun_mpi -s md_6_50ns.tpr -rerun md_6_50ns.gro gmxdump_mpi -e ener.edr ener_readme And in the dump of the ener_readme file, I have the following terms: Coul-SR:Protein-Protein -6.62324e+05 LJ-SR:Protein-Protein -5.64854e+04 Coul-14:Protein-Protein 4.04345e+05 LJ-14:Protein-Protein 3.29438e+04 Coul-SR:Protein-POPC -1.97403e+03 LJ-SR:Protein-POPC -4.64531e+03 Coul-14:Protein-POPC 0.0e+00 LJ-14:Protein-POPC 0.0e+00 ...etc There is neither a Coul-recip nor a Coul-LR term. So, I was wondering about it. The Coul-recip is the reciprocal space term in a Ewald summation calculation, right? I want the total potential energy of the protein. How would I go about that? Thanks. On Wed, Jan 15, 2014 at 7:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/15/14, 7:14 AM, rajat desikan wrote: Hi All, I was wondering about the long range electrostatics while calculating single point energies. I did a cursory calculation for a protein in water (PME) and found that the LR electrostatic terms were zero. I know that the per-particle decomposition of the LR electrostatics is non trivial. I was wondering if there is a way to do it in Gromacs? Was the Coul-recip term actually zero, or were you looking at Coul-LR? The two terms mean very different things. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] non-native contatcs
Hi, I have never done this before. But is this a possibility? http://www.pymolwiki.org/index.php/Contact_map_visualizer On Wed, Jan 15, 2014 at 8:41 PM, bipin singh bipinel...@gmail.com wrote: Hello Dr. Justin, Yes, there is no in-built module in Gromacs to get the information about native contacts during the simulation, but I think it can be done using the following resources outside the Gromacs: http://pythonhosted.org/MDAnalysis/documentation_pages/analysis/contacts.html http://www.multiscalelab.org/utilities/RMSDTTNC On Wed, Jan 15, 2014 at 7:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/15/14, 7:11 AM, bipin singh wrote: First define and calculate the native contacts (contacts which were present in native reference structure and exist for significant amount of time during simulation). Then you can identify the contacts which exist for significant amount of time but were not present in native reference structure (which may correspond to non-native contacts). Can you actually do this within Gromacs, or outside software? I'd be curious to know. -Justin On Wed, Jan 15, 2014 at 1:05 PM, suhani nagpal suhani.nag...@gmail.com wrote: Greetings I'm studying protein unfolding by CTMD and REMD simulations to capture the intermediate states. I want to calculate the non-native contacts formed during the intermediate state. Suggestions please Thanks Suhani Proteomics and Structural biology Lab CSIR-IGIB -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. 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 == -- 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. -- *Thanks and Regards,Bipin Singh* -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Calculating atom charges for ester
Hi, Here you go! http://pubs.acs.org/doi/abs/10.1021/jp003919d On Fri, Dec 13, 2013 at 8:42 PM, pp0ta187 p...@live.com wrote: Thank you Justin for a quick response. Although, I can not find the spoken reference in the manual, could you please point in which version is it? -- View this message in context: http://gromacs.5086.x6.nabble.com/Calculating-atom-charges-for-ester-tp5013305p5013310.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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Strange trjconv error
Hi All,
I have a NPT NAMD trajectory of a membrane-protein that I want to analyze
in gromacs 4.6.3. (g_density). I used catdcd to convert the .dcd to .pdb
and generated a .top from the .psf using topotools in vmd. I then generated
a .tpr using grompp
When I do any simple gromacs command like:
trjconv -f 130ns-141ns.pdb -s ref.tpr -o 130ns-141ns.xtc
I get the following error:
Fatal error:
An input file contains a line longer than 4096 characters, while the buffer
passed to fgets2 has size 4096. The line starts with: '20s'
wc -L ref.tpr
20344 ref.tpr
The gmxdump of the .tpr along with grep gave me the offending line. It is
essentially the protein description:
atom[ 0]={type= 0, typeB= 0, ptype=Atom, m= 1.40067e+01,
q=-6.0e-01, mB= 1.40067e+01, qB=-6.0e-01, resind=0, atomnumber=
-1}
atom[ 1]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-1.0e-01, mB= 1.20107e+01, qB=-1.0e-01, resind=
0, atomnumber= -1}
atom[ 2]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-3.5e-01, mB= 1.20107e+01, qB=-3.5e-01, resind=
0, atomnumber= -1}
atom[ 3]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-3.5e-01, mB= 1.20107e+01, qB=-3.5e-01, resind=
0, atomnumber= -1}
atom[ 4]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-3.5e-01, mB= 1.20107e+01, qB=-3.5e-01, resind=
0, atomnumber=
-1}...
Any idea about how to proceed. I am quite stumped.
Thanks.
--
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] Strange trjconv error
Dear Justin,
Thanks for the suggestion.
Producing a .trr in catdcd still failed because it apparently produces a
trajectory without a timestamp. So, I loaded the .dcd into vmd and saved
the coordinates in a .trr file. This worked like a charm :)
Note to self: Install gromacs with the vmd plugin next time...
On Tue, Dec 10, 2013 at 8:28 PM, Justin Lemkul jalem...@vt.edu wrote:
On Tue, Dec 10, 2013 at 8:55 AM, rajat desikan rajatdesi...@gmail.com
wrote:
Hi All,
I have a NPT NAMD trajectory of a membrane-protein that I want to analyze
in gromacs 4.6.3. (g_density). I used catdcd to convert the .dcd to .pdb
and generated a .top from the .psf using topotools in vmd. I then
generated
a .tpr using grompp
When I do any simple gromacs command like:
trjconv -f 130ns-141ns.pdb -s ref.tpr -o 130ns-141ns.xtc
I get the following error:
Fatal error:
An input file contains a line longer than 4096 characters, while the
buffer
passed to fgets2 has size 4096. The line starts with: '20s'
Unfortunately this is an output bug, so the '20s' is not actually useful to
you. Looks like something needs to be fixed in fgets2().
wc -L ref.tpr
20344 ref.tpr
The gmxdump of the .tpr along with grep gave me the offending line. It is
essentially the protein description:
atom[ 0]={type= 0, typeB= 0, ptype=Atom, m= 1.40067e+01,
q=-6.0e-01, mB= 1.40067e+01, qB=-6.0e-01, resind=0,
atomnumber=
-1}
atom[ 1]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-1.0e-01, mB= 1.20107e+01, qB=-1.0e-01, resind=
0, atomnumber= -1}
atom[ 2]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-3.5e-01, mB= 1.20107e+01, qB=-3.5e-01, resind=
0, atomnumber= -1}
atom[ 3]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-3.5e-01, mB= 1.20107e+01, qB=-3.5e-01, resind=
0, atomnumber= -1}
atom[ 4]={type= 0, typeB= 0, ptype=Atom, m=
1.20107e+01, q=-3.5e-01, mB= 1.20107e+01, qB=-3.5e-01, resind=
0, atomnumber=
-1}...
Any idea about how to proceed. I am quite stumped.
The problem is not in the .tpr file, it is in the .pdb file. Something
about its format is bad. Why not use catdcd to produce a .trr file
instead?
-Justin
--
==
Justin A. Lemkul, Ph.D.
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
==
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Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] heating
Hi Kiana, I always heat from 5 K to 300 K with ref_t=300 (ending temp) and gen_temp=5 (starting temp). 5 K is as good as starting at 0 K for my systems. Hope that helps. Regards, On Wed, Dec 4, 2013 at 12:18 PM, kiana moghaddam ki_moghad...@yahoo.comwrote: Dear Jastin Thanks very much for your reply, when I heat system from 0 to 300 K with simulated annealing, ref_t =300 is correct? Best Regards On Tuesday, December 3, 2013 5:53 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/3/13 2:17 AM, kiana moghaddam wrote: Dear GMX Users I want to run NVT equilibration and NPT equilibration (after NVT) and want to increase temperature gradually i.e. from 0 to 300 K over 100 ps, but I have some questions about this process: when I use simulated annealing in NVT as following annealing_time = 0 15 30 45 60 80 100 annealing_temp = 0 50 100 150 200 250 300 I don't know how to change gen_temp. Should gen_temp be 0 or 300 K? Generating velocities and then immediately freezing (in the strictest of sense) the system is likely not going to be stable or effective because the thermostat will go haywire trying to compensate for such a drastic change in temperature. It is an interesting question, because how does one generate velocities at 0 K? Theoretically, there are none. I would suggest setting gen_temp to 0; you can check the .tpr (via gmxdump) to see if any velocities are present, but even if they are they should be very small and largely irrelevant. The annealing protocol will warm the system relatively quickly, so even after a few dynamics steps, you will have small velocities within the system. At the first time, I did not use simulated annealing. I prepared 7 mdp files that in the first mdp file, I set nsteps=0, gen_temp=0, ref_t=0, then I use the output from first NVT equilibration for the second input. I repeat this to reach 300 K (in the second step nsteps=7500(*0.002=15), gen_temp=50, ref_t=50). I 'm not sure whether this process is correct? Well, it works, but it's laborious and unnecessary because you're just manually doing what simulated annealing is doing. -Justin -- == Justin A. Lemkul, Ph.D. 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 == -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] Coulombic potential modifiers in Gromacs 4.6.4.
Hi Mark, Thanks for the answer. I have a few doubts. 1) The whole potential is shifted by the value that it would otherwise have had at the cut-off. Doesn't this reduce the well-depth/epsilon for the LJ potential (same artifact as shifted LJ)? Will the long range corrections/DispCorr correct for this? 2) This is cosmetic in MD, unless you plan to compute based upon the energies. I am not very clear on this. Are there situations when I should not be using this? I can understand that shifted potentials cause difficulties in sensitive cases like near gas-liquid critical points, etc. Are there bio-molecular situations that one should be cautious about? 3) How would these modifiers affect the simulation in the presence of an external electric field? Thanks, I appreciate your time. The manual did not have the answers I need. On Fri, Nov 22, 2013 at 10:03 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Nov 21, 2013 9:20 AM, rajat desikan rajatdesi...@gmail.com wrote: Hi All, I was wondering about the coulomb-modifier = Potential-shift-Verlet option in conjunction with the Verlet cut-off scheme and PME. I can understand that vdw-modifier = Potential-shift-Verlet shifts the truncated LJ tail by a constant so that the potential is the integral of the force. No, see http://manual.gromacs.org/online/mdp_opt.html#el. The whole potential is shifted by the value that it would otherwise have had at the cut-off. This is cosmetic in MD, unless you plan to compute based upon the energies. Whether something else is trying to compensate for the missing long-range interactions has nothing to do with it. Mark What does the coulomb-modifier do? We are accounting for the long range coulombic interactions using reciprocal space sums in PME, right? What exactly is the shift here? Thanks -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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.
