[gmx-users] Segmentation Fault (Address not mapped)

;>> >>>>>>>>>>> I used cutoffs of 2 nm & 5 nm >>>>>>>>>>>> for my system so ensure the cutoff occured at a distance where the >>>>>>>>>>>> potentials were stabalized (not changing). I gue

[gmx-users] Segmentation Fault (Address not mapped)

ion list for GROMACS users Message-ID: <4a6e2092@vt.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Darrell Koskinen wrote: Hi Justin, With regard to your comment about using other force fields for my simulation of graphene surrounded by ammonia gas, are refe

[gmx-users] Segmentation Fault (Address not mapped)

is stable? Thanks again. Darrell Date: Tue, 04 Aug 2009 12:14:07 +1000 From: Mark Abraham Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users Message-ID: <4a77996f.9070...@anu.edu.au> Content-Type: text/plain; charset=windows-1252; format=

[gmx-users] Assigning Improper Dihedrals to an Index Group

gmentation Fault (Address not mapped) To: Discussion list for GROMACS users Message-ID: <4a6e2092@vt.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Darrell Koskinen wrote: Hi Justin, With regard to your comment about using other force fields for my simulation of graphe

[gmx-users] Improper Dihedrals

Dear GROMACS Gurus, I assigned improper dihedrals to my graphene structuure but still see it vibrating. Is this to be expected? I thought the purpose of improper dihedrals was to keep planar structures planar. Here is a copy of a couple of sections of my topology file after assigning the impr

[gmx-users] Determining the energy of an individual atom.

Dear GROMACS Gurus, In my simulation of a graphene structure surrounded by an ammonia gas, I am not seeing any adsorption of the ammonia molecules onto the surface of the graphene structure. I am wondering if the reason I am not seeing any absorption is because the graphene lattice is vibrating

[gmx-users] Determining the energy of an individual atom

Subject: Re: [gmx-users] Determining the energy of an individual atom. To: Discussion list for GROMACS users Message-ID: <4a823a10.6010...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Dear GROMACS Gurus, In my simulation of a graphene str

[gmx-users] Determining the energy of an individual atom

GROMACS users Message-ID: <4a8256e7.2030...@xray.bmc.uu.se> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Dear GROMACS Gurus, In my simulation of a graphene structure surrounded by an ammonia gas, I am not seeing any adsorption of the ammonia molecule

[gmx-users] Freezing part of a structure

Dear GROMACS Gurus, I tried to freeze two ends of a graphene structure (Grph) by assigning the HA atoms, at two ends of the graphene lattice, their own residue name (Frze) and residue number (210) in the .gro file. Before the assignment, the HA atoms belonged to the same residue as the CA atoms

[gmx-users] Graphene Sheet Rolling up into CNT

Hey GROMACS Gurus, I was wondering if you could enlighten me. I performed a simulation of a graphene sheet in an ammonia gas at 240K using ffoplsaa parameters and see that the graphene sheet begins to curl up into what appears to be a nanotube. I did not run the simulation long enough to actual

[gmx-users] ERROR: invalid enum 'xy' for variable pbc, using 'xyz'

Dear GROMACS Gurus, I am trying to create an infinite sheet of graphene using periodic boundary conditions. I created a sheet which fills the entire xy plane and thought that all I needed to do was put the line "pbc=xy" into the mdp file. However, when I run the simulation, I get the following

[gmx-users] Periodic Boundary Conditions & Location of Atoms Near Box Edges

Dear GROMACS Gurus, In order to correctly model an infinite graphene sheet using periodic boundary conditions, should the box edges be located at the midpoints between the atomic bonds? Thanks. Darrell ___ gmx-users mailing listgmx-users@gromacs

[gmx-users] No default Angle types

Dear GROMACS Gurus, I received the following error when running grompp: / ERROR 0 [file "graphene.top", line 392284]: No default Angle types / I believe this error is referring to the fact that there was no definition of an angle type for the following combination of atoms: HA CA CT since line

[gmx-users] 1-4 interaction between atoms in PBC mode

Dear GROMACS-ians, I have created an infinite graphene sheet and upon running grompp, I get the following response: /Warning: 1-4 interaction between 10085 and 10445 at distance 19.679 which is larger than the 1-4 table size 1.000 nm Warning: 1-4 interaction between 9244 and 9963 at distance 1

[gmx-users] Re: 1-4 interaction between atoms in PBC mode

Hi Omer, The atoms in question are part of a graphene sheet and are located at two opposite ends of the box. They should not move as they are bound inside the graphene sheet. The initial separation between these atoms is 19.678 nm, which is the same distance as in the warning message. So the p

[gmx-users] 1-4 interaction between atoms in PBC mode

t; Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Dear GROMACS-ians, I have created an infinite graphene sheet and upon running grompp, I get the following response: /Warning: 1-4 interaction between 10085 and 10445 at distance 19.679 which is larger than

[gmx-users] 1-4 interaction between atoms in PBC mode

te: Tue, 22 Sep 2009 15:07:03 +1000 From: Mark Abraham Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode To: Discussion list for GROMACS users Message-ID: <4ab85b77.10...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: >

[gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

Hi, I see that the Lennard Jones parameters for the N & H atoms in ammonia, represented by opls_127 and opls_128 in the file ffoplsaanb.itp are: opls_127 NT 7 14.00670-1.020 A3.42000e-01 7.11280e-01 opls_128 H 1 1.00800 0.340 A0.0e+00 0.0e

[gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

aa To: Discussion list for GROMACS users Message-ID: <4adc1e3a.8010...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi, I see that the Lennard Jones parameters for the N & H atoms in ammonia, represented by opls_127 and opls_128 in

[gmx-users] Adsorption energy of a single molecule

Hi Justin, Thanks for the suggestion. I looked through the GROMACS manual and the only method I can see of obtaining the adsorption energy between an adsorbed ammonia molecule and the graphene sheet would be to create an index file that assigns a separate index for each ammonia molecule, run t

[gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

format=flowed Justin A. Lemkul wrote: Darrell Koskinen wrote: I looked through the ffoplsaanb.itp file and see that all the H atoms except for the following four have zero LJ parameters: HC OPLS_140 alkane H HA OPLS_146 Benzene H H4 OPLS_345 Cytosine H-C6 H5 OPLS_355 Adenine & Gu

[gmx-users] Adsorption energy of a single molecule

energy of a single molecule To: Discussion list for GROMACS users Message-ID: <4aed7c54.2080...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi Justin, Thanks for the suggestion. I looked through the GROMACS manual and the only method I

[gmx-users] Lennard Jones Parameters for Ammonia in ffoplsaa

MACS users Message-ID: <4aed36ba.1040...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi Mark, I thought opls_127 and opls_128 were the representative atoms to use for ammonia. Please correct me if I am wrong. I don't kn

[gmx-users] Adsorption energy of a single molecule

orption energy of a single molecule To: Discussion list for GROMACS users Message-ID: <4aee27f0.50...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: > Hi Justin, > In my simulation, I have just over 100 ammonia molecules and, of t

[gmx-users] Determining density of a gas in a simulation

Dear GROMACS Gurus, I wanted to determine the density of the ammonia gas in my simulation and compare this to the reference values and thought I could use g_density for this purpose. I recall being told that I need to perform a NPT simulation and achieve equilibrium. How do I perform an NPT si

[gmx-users] Is pressure coupling required in a simulation?

Hi, I was wondering if you could tell me if pressure coupling is always required in a simulation? The reason I am asking is because when I run my simulation with pressure coupling disabled my simulation completes without any warnings, but when I run my simulation with pressure coupling enabled

[gmx-users] Can not find forcefield for atom C4-1 with 0 bonds

Hi, I am trying to create a topology file from a .gro file. When I run x2top with methane (C4 opls_066) in my .gro file, I receive the following warning: /Can not find forcefield for atom C4-1 with 0 bonds/ I have included the following line in the ffoplsaa.n2t file, which resides in my workin

[gmx-users] Constraints & Restraints

Hi Tsjerk, So then, if I understand correctly, setting "constraints = all-bonds" is not as realistic as setting "constraints = none", since the latter will allow for flexible (e.g. harmonic) behavoir which is more realistic than fixing the bond to a certain distance, correct? Thanks. Darrell

[gmx-users] Adsorption energy of a single molecule

ion energy of a single molecule To: Discussion list for GROMACS users Message-ID: <4aee4387.40...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi Justin, Since I cannot use the original .tpr file, then do I need to run grompp with the n

[gmx-users] Constraints & Restraints

. Darrell Date: Thu, 12 Nov 2009 14:16:06 +0100 From: Ran Friedman Subject: Re: [gmx-users] Constraints & Restraints To: Discussion list for GROMACS users Message-ID: <4afc0a96@bioc.uzh.ch> Content-Type: text/plain; charset=ISO-8859-1 Erik Marklund wrote: > Mark Abraham skrev:

[gmx-users] Adsorption energy of a single molecule

To: Discussion list for GROMACS users Message-ID: <4afb4be0.1020...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Hi Justin, So when I create the index file with the molecule and the graphene sheet and run g_energy, is the adsorption

[gmx-users] Diffusion of Ammonia Gas

Dear GROMACS-ites, I am trying to determine whether OPLS can be used to model gas-phase ammonia. To this end, I created a 30 nm^3 box with 729 ammonia molecules in it, performed energy minimization, and ran a simulation at 298K & 1.01325 bar for 20 ps followed by another simulation of 20 ps dur

[gmx-users] Unexpected behavior of g_msd

Dear GROMACS-ites, I am a little confused by the behavior of g_msd. I have a trr file with data points from t=0 to t=100 ps and thought that the following command would perform a regression for the data points between t=60 ps and t=100 ps to determine the diffision constant of the ammonia gas i

[gmx-users] Unexpected behavior of g_msd

at the counting for the regression is done on the frames read: 100 - 60 = 40 ps Then 4 and 35.9 would correspond to 64 and 95.9. The answer is in the code... But using a subtrajectory may give you good hint. Hope it helps, Tsjerk On Wed, Nov 25, 2009 at 7:42 AM, Darrell Koskinen wrote: > Dea

[gmx-users] Unexpected behavior of g_msd

, Parkville VIC 3010 > dallas.war...@pharm.monash.edu.au > +61 3 9903 9167 > - > When the only tool you own is a hammer, every problem begins to resemble > a nail. > > > > -Original Message----- > > From: gmx-users-boun...@gromacs.or