[gmx-users] Assignment of Atoms to Charge Groups in x2top

Hi All, I am wondering how atoms are assigned to charge groups when a .gro file is run through x2top. I have a structure in a .gro file where not all the atoms in sequential order are adjacent to one another, yet x2top seems to assign them to the same charge group. For example, atoms 1301 to 1348

[gmx-users] How are bond parameters linked to atoms when using #include?

Hi All, I have just executed my first mdrun and it appears that the default bond parameters from x2top were used instead of the bond parameters from the oplsaa force field files which are included in my .top file. Here is an extract from my .top file with the include statement: **

[gmx-users] No default Angle types

Dear All, I ran grompp and was presented with the following error: ERROR 0 [file "graphene_nm_test.top", line 51217]: No default Angle types Line 51217 of the topology file is: 5116 5115 5117 1 and atoms 5115 to 5117 are defined in the topology file as: 5115 opls_145 1 Grph C 4859 -0.12 12.

Re: [gmx-users] No default Angle types

Hi Justin, Thanks for the quick reply. Yes, I was also thinking about using a different atom type such as the alkane types you mentioned below. However, when I thought about how I can include these atom types in my .n2t file, I recognized that this might cause a potential problem since now I woul

[gmx-users] Molecule Jumps

Hi All, I have an array of molecules above a grapehene sheet in my simulation. However, when I look at my trajectory file (.trr) in VMD the array of molecules is split into 4 sections with each section located at what looks to be the corners of the simulation box. And the graphene sheet does not s

[gmx-users] Re: Molecule Jumps

Hi All, I just wanted to let you know how I resolved my problem, in case anyone else experiences a similar problem in the future. My structure spanned all four quadrants around the origin (i.e. the 4 vertices of my structure were (-x, -y), (-x,y), (x,-y), & (x,y)). I think because it spanned all

[gmx-users] Website Problem

Dear GROMACS Website Administrator, I have been trying to view your website a couple of times lately and each time I was presented with the same message: Site settings could not be loadedWe were unable to locate the API to reque

[gmx-users] Website Problem

Hi Mark, Thanks for your suggestion. I opened up the web page associated with the link you provided below (http://oldwww.gromacs.org/) but when I clicked on "search" on this web page, I was once again presented with the response "Site settings could not be loaded.." Could you please let me kn

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

Dear GROMACS Gurus, I am experiencing a segmentation fault when mdrun executes. My simulation has a graphene lattice with an array (layer) of ammonia molecules above it. The box is three times the width of the graphene lattice, three times the length of the graphene lattice, and three times the he

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

Hi Mark, I added the energy group exclusions as indicated in your previous response but am still experiencing the same problem. I looked at the .log files and see that in one log file it tells me that my box is exploding. However, I do not have many molecules in my simulation and therefore do not

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

Hi Mark, I used editconf on my .gro file with zero space between my solvent and the box and the resulting box had the exact same dimension as the initial box. I also performed a number of simulation runs with different mdp parameters hoping this would provide me some indication of the cause of the

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

Hi Justin, I was experiencing the problem before someone suggested using editconf so I do not think the problem is being caused by editconf. But anyway here is my editconf command. Let me know if you a source of error in this command line. editconf -f graphene.gro -n index.ndx -o graphene_ec.gro

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

Hi Justin, I was experiencing the problem before someone suggested using editconf so I do not think the problem is being caused by editconf. But anyway here is my editconf command. Let me know if you a source of error in this command line. editconf -f graphene.gro -n index.ndx -o graphene_ec.gro

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

Hi Mark, Yes, I know that the box dimensions are defined in the last line of the .gro file and I have defined these dimensions as 38 nm x 38 nm x 38 nm in the .gro file. I looked through my .gro file to ensure none of the atoms had coordinates outside the 38x38x38 box. While I was reviewing the f

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

Hi Mark, I do not do any equilibration, I only do energy minimization as in the "GROMACS Tutorial for Solvation Study of Spider Toxin Peptide". Please let me know if I need to do equilibration and what is the difference between energy minimization and equilibration as this is not clear to me. Her

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

Hi Justin, Thanks for the explanation of the difference between EM & equilibration. Since in my model, I: (i) only have the graphene sheet and ammonia molecules spaced reasonably far apart from each other (1332 NH3 molecules in a 38x38x38 box) and from the graphene sheet (distance between the clos

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

Hi Justin, I froze the graphene sheet because, prior to freezing it, I noticed that it was vibrating and thought that maybe its vibration was not allowing the NH3 molecules to adsorb (bond) to it. But after freezing the graphene sheet, I see that see that NH3 molecules are still not bonding to it.

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

Hi Justin, I am using the ffoplsaabon.itp parameters for: bonds (CA-CA, CA-CT, CA-HA, CT-HC, H-N3) angles (CA-CA-CA, CA-CA-HA, CA-CT-HC, H-N3-H) dihedrals (X-CA-CA-X, X-CA-CT-X) I am using the ffolpsaanb.itp VdW parameters for H & N3 And I am using the VdW parameters found in the paper "A Second

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

Hi Justin, I am using version 3.3.3 and read through the version 3.3 manual but do not see an option to set "pbc = full" in this manual. I only see options to set pbc to "xyz" or "no". Will setting pbc=full be recognized in GROAMCS version 3.3.3 and will this solve my problem? Thanks. Darrell >

[gmx-users] Adsorption energy of a single molecule

Dear GROMACS Gurus, Is it possible to determine the adsorption energy of a single molecule in a simulation? My simulation has a large number of gas phase molecules distributed throughout a box with some molecules adsorbed on a graphene sheet. I would like to compare the adsorption energy of a sing

[gmx-users] Constraints & Restraints

Hi, I just have a quick question on contraints and restraints. My understanding is that "constraints" fix the position of an atom in space and "restraints" restrain the deviation of the atom's position from its equilibrium point. Is that correct? If so, then I am a little confused by the purpose o

[gmx-users] Unexpected behavior of g_msd

Hi Berk, I am thinking that you mean that MSD is a function of the time differences and the number of time differences. In other words, if the simulation is too short, then GROMACS would not have enough time differences to accurately calculate a diffusion constant since the slope of the msd versus

[gmx-users] Fatal error: Could only find a forcefield type for 106 out of 270 atoms

Could you please let me know why GROMACS is able to find forcefields for only 106 of the 270 atoms. My .gro file is a model of a graphene structure with 211 equally spaced carbon atoms with the remaining hydrogen atoms also equally spaced from the carbon atoms to which they are bonded. Here is a s

[gmx-users] x2top & Encad all-atom force field (vacuum) not recognizing bonds

Dear All, I have been trying to determine why I am experiencing problems when I run a gromacs file through x2top. I have checked my gromacs file with VMD to ensure that the file is correct and VMD validates that my file is correct as I see the intended structure. Thus, the atoms are indeed located

Re: [gmx-users] x2top & Encad all-atom force field (vacuum)

>Date: Wed, 01 Apr 2009 22:38:28 +0200 >From: David van der Spoel >Subject: Re: [gmx-users] x2top & Encad all-atom force field (vacuum) > not recognizing bonds >To: Discussion list for GROMACS users >Message-ID: <49d3d0c4.4040...@xray.bmc.uu.se> >Content-Type: text/plain; charset=ISO-8

Re: [gmx-users] x2top & Encad all-atom force field (vacuum)

Dear All, I am resubmitting my question below as I did not receive a response and am thinking that my previous e-mail was not recognized by the system or missed. Could someone please provide me with an answer to my questions below? Many thanks. Darrell Koskinen On 4/2/2009, "" <> wrote: >>Date

[gmx-users] Re: gmx-users Digest, Vol 60, Issue 40

Dear All, Please see my questions inline below. Thanks again for your help. Darrell >darre...@ece.ubc.ca wrote: >> Dear All, >> I am resubmitting my question below as I did not receive a response and >> am thinking that my previous e-mail was not recognized by the system or >> missed. Could som

Re: Re: [gmx-users] x2top & Encad all-atom force field (vacuum)

Dear All, I forgot to change the subject line of my previous post from "Re:gmx-users Digest, Vol 60, Issue 40" to something more indicative of my post, so I am resubmitting it with the appropriate subject title. Please disregard my earlier post. Please see my questions inline below. Thanks. Dar

[gmx-users] x2top: duplicate bond, angle, & dihedral parameters; missing VdW parameters

Dear All, I ran the x2top command and successfully generated a topology. However, the topology file has duplicate bond, angle, and dihedral parameters and missing Van der Waals parameters. I am including sections of my topology file for your perusal. Please let me know why this is occurring and ho

[gmx-users] Missing VdW Parameters

Dear All, I successfully ran the x2top command (x2top -ff select -f graphene_nm.gro -o graphene_nm.top) and generated a topology using ffoplsaa, but my topology is missing VdW parameters, which I thought should be appearing in the [ pairs ] section of the topology file. I thought that x2top would

Re: [gmx-users] Missing VdW Parameters

Hi David, Yes, indeed, the topology file does have the #include statement. Here is an extract from the topology file: *** ; Include forcefield parameters #include "ffoplsaa.itp" [ moleculetype ] ; Namenrexcl ICE

[gmx-users] Missing VdW Parameters

Hi All, I did not receive a response yet for my question below, so I am submitting it once again. Thanks again in advance for your help. Darrell On 4/12/2009, "" <> wrote: >Hi All, >Yes, indeed, the topology file does have the #include statement. Here is >an extract from the topology file: >**