[gmx-users] Questions regarding converting .GRO files to .TOP files
Dear GROMACS users:
I have a few questions about converting the .GRO files to .TOP files. I
first used Python to create a sheet of graphene layer by using the
following Python codes:
from ase import *
from ase.structure import graphene_nanoribbon
from ase io.import*
gnr1 = graphene_nanoribbon(8,8, type='armchair')
write('graphene.pdb', gnr1, format='pdb')
Second, I used the following codes to convert the PDB file to GRO file for
the cathode layer:
editconf -f graphene.pdb -o graphene_cathode.gro
Third, I used the following codes to convert the PDB files to GRO file for
the anode layer:
editconf -f graphene.pdb -translate 0 5.0 -o graphene_anode.gro
Fourth, I combined the cathode layer and the anode layer to one complete
structure according to the following code:
genbox -cs graphene_cathode.gro -cp graphene_anode.gro -maxsol 5000 -box 3
1 3 -o electrodes.gro
Fifth, I converted the electrode gro file to top file according to the
following code:
g_x2top -f electrodes.gro -ff cnt_oplsaa -o device.top
GROMACS showed that there are carbon atoms force field that can not be
found in the atomname2type.n2t file.
part of the error message is shown as the following:
Can not find forcefield for atom C-447 with 6 bonds
Can not find forcefield for atom C-448 with 5 bonds
Fatal error:
Could only find a forcefield type for 364 out of 512 atoms.
My atomname2type.n2t file consists of the following:
C opls_145 -0.12 12.011 3 C 0.150 C 0.150 H 0.108
C opls_145 -0.12 12.011 3 C 0.133 C 0.150 O 0.140
C opls_145 0.0 12.011 3 C 0.140 C 0.140 C 0.140
C opls_145 0.0 12.011 2 C 0.140 C 0.140
However, the TOP files for the cathode layer or the anode layer can be
converted from the GRO files without any error as the following:
g_x2top -f graphene_cathode.gro -ff cnt_oplsaa -o graphene_cathode.top
g_x2top -f graphene_anode.gro -ff cnt_oplsaa -o graphene_anode.top
can people explain why? What is the reason behind the error message that I
got when converting the GRO file of two combined layer of graphene to the
TOP file while the same atomname2type.n2t file is used?
Thank you very much!
Andy
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[gmx-users] GROMACS 5.0 official release
Hi GROMACS users, The official release of GROMACS 5.0 is available! What new things can you expect? * GROMACS now uses a combination of *C++98* and C99, so you will need a working C++ compiler that is intended to work with your C compiler * Building GROMACS now requires *CMake version 2.8.8*, which will mean some of you will need to update your version in order to build GROMACS. * The native GPU port available in GROMACS 4.6 supports a wider range of simulation types, and now requires CUDA 4.0 * The *Verlet cut-off scheme is now the default* in GROMACS. One of our design principles is that GROMACS will do correct simulations by default, and the use of this scheme makes that easy and fast. The group cut-off scheme will be removed in a future version, so start planning for that! * You can now treat *Lennard-Jones interactions with PME*, which is expected to provide a much better treatment of spatially heterogeneous long-ranged dispersion interactions at cost comparable to that of a cutoff. LJPME is supported for both cut-off schemes, and almost all kinds of simullations * GROMACS deploys the Random123 stateless random-number generator * GROMACS now uses the stochastic dynamics (sd1) integrator of Goga & Berendsen * GROMACS tools are now bundled together into *just two binaries* - mdrun and gmx. The latter contains most of the tools familiar to you, perhaps with new names, and a couple of new ones. For the time being, the install procedure will also create symbolic links so that your old scripts will keep working for a time, but these will go away at some future point! * There is support for the new TNG compressed trajectory format * GROMACS contains a feature for "computational electrophysiology" simulations, to simulate a steady-state ion concentration difference between compartments of a double membrane * GROMACS supports some special interactions for coarse-grained interactions with Martini force fields * GROMACS support for Interactive Molecular Dynamics (IMD) * A handful of the tools have been re-implemented using a *new C++ analysis framework*, which we hope will provide a better platform for maintaining and adding to their functionality in the future. * There is an enhanced testing suite, with *unit tests* for most new C++ code. * There is preliminary support for Intel Xeon Phi (only in native mode, and performance will only be slightly improved) * GROMACS has removed support for particle decomposition - the simulation types that required it are now limited to a single MPI rank (but perhaps multiple OpenMP threads) Please see the link to the release notes below for more details. All the content of GROMACS 4.6.6 (whose release is imminent) is present, apart from features that have been removed. You can find the code, manual, release notes, installation instructions and test suite at the links below. ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ftp://ftp.gromacs.org/pub/manual/manual-5.0.pdf http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0 http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0 http://gerrit.gromacs.org/download/regressiontests-5.0.tar.gz Happy simulating! Mark Abraham GROMACS development manager -- 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 calculate Box Vectors in the last line of the .gro file?
On 6/29/14, 3:06 PM, Todor Antonijevic wrote: Hi, I cannot obtain the last line (box vectors *1.82060 1.82060 1.82060*) of the .gro file. *Can anyone explain me how the last line is calculated?* The example is from the manual: "MD of 2 waters, t= 0.0 6 1WATER OW11 0.126 1.624 1.679 0.1227 -0.0580 0.0434 1WATER HW22 0.190 1.661 1.747 0.8085 0.3191 -0.7791 1WATER HW33 0.177 1.568 1.613 -0.9045 -2.6469 1.3180 2WATER OW14 1.275 0.053 0.622 0.2519 0.3140 -0.1734 2WATER HW25 1.337 0.002 0.680 -1.0641 -1.1349 0.0257 2WATER HW36 1.326 0.120 0.568 1.9427 -0.8216 -0.0244 *1.82060 1.82060 1.82060*" This is just an example of what a .gro file might look like. Setting up a box is very easy with editconf; it does all the work for you. See basic tutorials for information. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How to calculate Box Vectors in the last line of the .gro file?
Hi, I cannot obtain the last line (box vectors *1.82060 1.82060 1.82060*) of the .gro file. *Can anyone explain me how the last line is calculated?* The example is from the manual: "MD of 2 waters, t= 0.0 6 1WATER OW11 0.126 1.624 1.679 0.1227 -0.0580 0.0434 1WATER HW22 0.190 1.661 1.747 0.8085 0.3191 -0.7791 1WATER HW33 0.177 1.568 1.613 -0.9045 -2.6469 1.3180 2WATER OW14 1.275 0.053 0.622 0.2519 0.3140 -0.1734 2WATER HW25 1.337 0.002 0.680 -1.0641 -1.1349 0.0257 2WATER HW36 1.326 0.120 0.568 1.9427 -0.8216 -0.0244 *1.82060 1.82060 1.82060*" Thank you very much -- 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] EDLC simulation using Gromacs
It is very easy. You apply an electric field and observe how DL is forming. Have fun. Dr. Vitaly V. Chaban On Fri, Jun 27, 2014 at 3:14 PM, Andy Chao wrote: > Dear Users, > > Would you please suggest a few examples of using GROMACS to simulate an > EDLC device? > > Thanks a lot! > > Andy > -- > 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.
