Manual section 4.2.13 maybe not enough. My potential functional shape is
much more complex. I need at least two different force constants as C6 and
C12 in LJ potential function in section 6.7.2.
I use this for block copolymer system. There is only two types of
monomer(e.g. A, B) and two types of bo
Justin A. Lemkul wrote:
Please file a bugzilla, uploading all of the input files needed to
reproduce the problem. It appears that you can cause LP2 to be assigned
an LP type if it is the first line in atomtypes.atp, but the mass and
charge are still nonsense. Certainly you can manually mod
On 8/12/2010 4:52 AM, Igor Marques wrote:
Hello everybody,
I've digging around the user manual, the website and the mailing list
archives and I'm afraid I might be missing something: does GROMACS
have some kind of /neutral plasma /as AMBER does?
You're probably referring to some descriptions
zhongjin wrote:
Hi all,
I want to know how to set a NVE simulation ? Now I can do a NVT or NPT
simulation.
tcoupl = no
pcoupl = no
http://www.gromacs.org/Documentation/Terminology/NVE
How to realize pressure scaling in one dimension and constant size
simulation in another? For ex
On 8/12/2010 1:30 PM, zhongjin wrote:
Hi all,
I want to know how to set a NVE simulation ? Now I can do a NVT or NPT
simulation.
It's the default, simply use neither T nor P coupling.
How to realize pressure scaling in one dimension and constant size
simulation in another? For exa
Hi all,
I want to know how to set a NVE simulation ? Now I can do a NVT or NPT
simulation.
How to realize pressure scaling in one dimension and constant size
simulation in another? For example,the simulation box size in the z-direction
was adjusted to maintain the constant pressure, whil
On 7/12/2010 6:34 PM, גדעון לפידות wrote:
Hi all,
Does anyone know of way I can use Gromacs to calculate the
disasociation constant of a calcium ion held by two loops in a protein
in water simulation? my starting point was a pdb file of the protein
with the bound ions in place. Eventually I wo
On 8/12/2010 4:07 AM, J. Nathan Scott wrote:
Hello all! I spent some time searching the archive and can't find an
answer to this question. Is there a replacement for the -rtpo option
for pdb2gmx? This option is mentioned in the v 4.5.3 (the version I am
using) manual (pg 115) but does not seem to
The nicelevel is simply the priority of the process, where 19 is the
lowest priority (ie most other programs will use the cpu before the
gromacs process does) and -20 the highest.
See man nice.
// Linus
On Tue, Dec 7, 2010 at 10:13 PM, GZ Zhang wrote:
> Hi, ALL
> I'm using "genbox" to crea
GZ Zhang wrote:
Hi, ALL
I'm using "genbox" to create a water box. There is a flag called
"-nice" which is described to be used to set the nicelevel.
What is nicelevel ? What does the default value "19" mean ? What if I
Google is your friend here.
would like to increase the decimal pl
Hi, ALL
I'm using "genbox" to create a water box. There is a flag called
"-nice" which is described to be used to set the nicelevel.
What is nicelevel ? What does the default value "19" mean ? What if I would
like to increase the decimal places (the default
is 3) of all numbers. Thanks.
Hello everybody,
I've digging around the user manual, the website and the mailing list
archives and I'm afraid I might be missing something: does GROMACS have some
kind of *neutral plasma *as AMBER does?
Or every simulation must have a net charge of 0.000 ?
Best regards,
Igor Marques
--
g
Dear Gromacs Users,
I am calculating entropy from QHA and Schlitters formula to determine the
entropy change in my proteinA-proteinB complex.
Since proA and proB are quite different in terms of number of residues, I am
little confused if I should divide the entropy value with the number of atoms
Hello all! I spent some time searching the archive and can't find an
answer to this question. Is there a replacement for the -rtpo option
for pdb2gmx? This option is mentioned in the v 4.5.3 (the version I am
using) manual (pg 115) but does not seem to work, and yields the error
"Invalid command li
Hi all
I have recently generated a PMF curve for pulling a guest molecule into
a host. The curve for this process appears fine. Analysis of the
histograms are also fine except that some histograms are not centred on
their r0 values in the barrier region. To circumvent this I increased
the force c
Jia Haitao wrote:
Hello, everyone
In gromacs user manual 6.7, they form non-bond potentials using table
files, What should I do if I want to use a new *Bond* potential?
The new bond potential combines two harmonic bond
potentials, Vb(r)=0.5K1(r-b1)^2+0.5K2(r-b2)^2. The first part is a
sta
Hello, everyone
In gromacs user manual 6.7, they form non-bond potentials using table files,
What should I do if I want to use a new *Bond* potential?
The new bond potential combines two harmonic bond
potentials, Vb(r)=0.5K1(r-b1)^2+0.5K2(r-b2)^2. The first part is a standard
harmonic potential.
Hi Leila,
I would try the other suggested options like catdcd or vmd. The script is a
pain and you would have to adapt it to work with DNA. It cost me a lot of
time.
I used g_hbond for residence time like this:
g_hbond -f 8_fullMD_CA.xtc -s 7_fullMD.tpr -n g_hbond.ndx -a 170 -num >
g_hbond.log
Dear gerrit sir,
thank you for your reply
Here I have got compilation error as follows
/root/gromacs-4.5.3/src/mdlib/.libs/libmd_d.a(qm_mopac.o):
In function `call_mopac_SH':
qm_mopac.c:(.text+0x2a7): undefined
reference to `domop_'
/root/gromacs-4.5.3/src/mdlib/
Dera gromacs users,
I am trying to do QMMM in the latest gromacs version :gromacs-4.5-beta2.
When I run DFT I got an error:
number of CPUs for gaussian = 1
memory for gaussian = 5000
accuracy in l510 = 8
NOT using cp-mcscf in l1003
Level of SA at start = 0
Segmentation fault
Are you tryin
no surface, no surface energy, just that simple...
check any colloid & surfaces textbook before you
try to calculate surface tension (and read the manual
as well, specially the section dealing with surface
coupling)
best
Andra
On Tue, Dec 7, 2010 at 9:28 AM, vinothkumar mohanakrishnan
wrote:
> No
You can try using vmd. It has a powerful language selection and it can
be used remotely.
There is one disadvantage: the trajectory MUST fit into memory since vmd
loads the trajectory into memory.
If this is not the case, you can use the script "bigdcd" that permits
to load one frame in memory
On 07/12/10 03:06, nishap.pa...@utoronto.ca wrote:
Quoting ms :
I did two different simulation. One with van der Waals attractive term
and one without van der Waals attractive term. And so to see the
difference between the LJ potential between the two simulation I wanted
to plot the LJ potential
Dear Oliver
very thanks for your help.
Justin's perl script is good for direct hydrogen bonds, while I want to
study water
mediated hydrogen bonds and residence time and occupation of them.
Are youe sure g_hbond give you residence time of hydrogen bonds?
before you said you used a script to cha
No.. i didn't do that. I just filled the box with 865 water molecules based
on my number density calculations and the box size is 3.255*3.255*2.545 and
performed energy minimisation followed by NVT and NPT equilibration. what
should i do now to get the correct surface tension?
Regards
Vinoth
2010
did you increase the size of the box in one direction in order
to create a water/vacuum interface on each side of the water
slab?
best,
Andre
On Tue, Dec 7, 2010 at 8:21 AM, vinothkumar mohanakrishnan
wrote:
> Hi all
>
> I want to calculate the surface tension of water using SPC model of water. I
I have previously used catdcd software for trajectory conversions between
gromacs-Amber.
Best Wishes
Shozeb
On 7 Dec 2010, at 10:57, "leila karami" wrote:
> Dear Oliver Grant
>
> thanks for your attention.
>
> I want to use amber tool for hydrogen bond analysis especially (water
> mediate
Hi Leila,
I've done this with g_hbond and g_bond. If you search the forums there is a
perl script available from Justin Lemakul that will do this for you. You can
do it manually too if you have only a few to look at. Its a little tricky
but a lot easier than traj conversion. :) I was able to get %
Dear Oliver Grant
thanks for your attention.
I want to use amber tool for hydrogen bond analysis especially (water
mediated hydrogen bonds and residence time and occupation of them).
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Ch
I suppose it depends on what kind of analysis you would like to do... I'm
not aware of any scripts for converting back from gmx into amber
trajectories but I have done this before when doing an mmpbsa calculation
using ambertools. As I only needed "snaphots" of the trajectory and not
energies or ve
Hi all
I want to calculate the surface tension of water using SPC model of water. I
searched the mailing list and there is no post on the surface tension of
water.I performed md simulation of 482 molecules of water in a triclinic
box. I got the average surface tension value of water (300K) as 38.3
Dear gromacs users,
>
> I am trying to do QMMM in the latest gromacs version :gromacs-4.5-beta2.
> When I run DFT I got an error:
>
> number of CPUs for gaussian = 1
> memory for gaussian = 5000
> accuracy in l510 = 8
> NOT using cp-mcscf in l1003
> Level of SA at start = 0
> Segmentation fault
Dera gromacs users,
I am trying to do QMMM in the latest gromacs version :gromacs-4.5-beta2.
When I run DFT I got an error:
number of CPUs for gaussian = 1
memory for gaussian = 5000
accuracy in l510 = 8
NOT using cp-mcscf in l1003
Level of SA at start = 0
Segmentation fault
Please could you
Hi, Mark,
I'll adopt your suggestion.
Thank you for your reply again.
Sincerely yours,
Hsin-Lin
On 7/12/2010 6:01 PM, Hsin-Lin Chiang wrote:
>/
/>>/ Ah, sorry, I didn't read you well enough.
/>>/
/>>/ I've just seen that GROMACS 4.5 introduced trjconv -round to address
/>>/ this kind of iss
On 7/12/2010 6:01 PM, Hsin-Lin Chiang wrote:
Ah, sorry, I didn't read you well enough.
I've just seen that GROMACS 4.5 introduced trjconv -round to address
this kind of issue. I suppose you will find trjconv -round -split
works for you.
Mark
Hi, Mark
Thank you for your suggestion.
I'm so
35 matches
Mail list logo