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
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
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
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
>
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
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.
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
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
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
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
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
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
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
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
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
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
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
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
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
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.
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:
**
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
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:
>**
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
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
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
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
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
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
>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
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
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
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