Dear All
I tried to run MD with ensemble based distance restrain. I set
disre=Ensemble and use -multi command argument in mdrun, according to the
manu. However, gromacs4.6 give me an error "Sorry, distance restraints with
ensemble averaging over multiple molecules in one system are not functional
Hey,
Residue numbers don't matter. You can reorder the .gro file to have all the
solvent at the end:
sed -e '/SOL/{H;d}' -e '${x;s/^\n//p;x}' file.gro
Note that this doesn't work with BSD sed, like on a Mac :p
Cheers,
Tsjerk
On Thu, Jan 10, 2013 at 1:34 PM, Justin Lemkul wrote:
>
>
> On 1/1
Hi James,
The default is non-mass weighted. If you want to relate the principal
components to normal modes, and want to obtain mode frequencies, you
(formally) need to include the masses.
Cheers,
Tsjerk
On Fri, Jan 11, 2013 at 7:46 PM, James Starlight wrote:
> Tsjerk, thanks for suggestion!
>
Tsjerk, thanks for suggestion!
By the way I've found in the pca.log ( that time pca was done on
trajectory as well as TRP ( not pdb) files as the inputs ):
Read 30 frames from cam_xray_coors_bb.pdb (time 1 to 30 ps)
Read reference structure for fit from x_ray.tpr
Analysis group is 'System' (575
Hello all,
I am trying to compare PME and shift electrostatics methods for my
hydrocarbon system. In both cases rlist = 1.35 , but in case
of PME rcoulomb= 1.35 while for shift **
rcoulomb= 1.1. I see no significant change (less than 1%) in
total system pot
On 1/11/13 7:18 AM, anna.duncan wrote:
Thank you for your reply.
You're right that I want to measure the protein-lipid interaction by
determining the length of time that the lipid is within a certain distance
of the protein. However, I also want to get a measure of the length of
time that th
On 1/11/13 9:34 AM, Sanku M wrote:
Hi Erik,
That statement was a typo. The simulation will be done in implicit solvent (
not in gas phase).
Sanku
From: Erik Marklund
To: Sanku M ; Discussion list for GROMACS users
Sent: Friday, January 11, 2013 5:04 A
On 1/11/13 1:10 PM, Miguel Ángel Mompeán García wrote:
The donors are two H atoms from the amide group of Gln residues. Thus,
I will try the -merge option. Thank for the comment.
I wonder if the following issue is affecting gromacs 4.5.5:
http://lists.gromacs.org/pipermail/gmx-users/2011-May/
The donors are two H atoms from the amide group of Gln residues. Thus,
I will try the -merge option. Thank for the comment.
I wonder if the following issue is affecting gromacs 4.5.5:
http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html
2013/1/11, Justin Lemkul :
>
>
> On 1/11/13 6:
Hi James,
You don't need a .tpr file. A .gro or .pdb file will do as well. Unless you
insist on doing mass-weighted PCA.
Cheers,
Tsjerk
On Fri, Jan 11, 2013 at 4:04 PM, James Starlight wrote:
> Dear Gromacs users!
>
>
> I want to perform Covariance analysis of my x-ray data sets via
>
> g_cova
Dear Gromacs users!
I want to perform Covariance analysis of my x-ray data sets via
g_covar -f trr.pdb -s x_ray.tpr -n index -o PCA_eigenval.xvg -v PCA_eigenvec.trr
where trr.pdb is the trajectory made from the 30 x-ray structures
(only c-alpha atoms were selected. How I could obtain x_ray.tpr
Hi Erik,
That statement was a typo. The simulation will be done in implicit solvent (
not in gas phase).
Sanku
From: Erik Marklund
To: Sanku M ; Discussion list for GROMACS users
Sent: Friday, January 11, 2013 5:04 AM
Subject: Re: [gmx-users] mdp option fo
Hi all,
When calculating the average number of hbonds during a simulation, does the
program g_hbond contemplate the possibility of an atom involved in two
hbond?
If I visualize the structures with molden, setting the same cutoff
criterion for hbonding than g_hbond utilizes, I found out that some O
On 1/11/13 6:23 AM, Miguel Ángel Mompeán García wrote:
Hi all,
When calculating the average number of hbonds during a simulation, does the
program g_hbond contemplate the possibility of an atom involved in two
hbond?
If I visualize the structures with molden, setting the same cutoff
criterion
Thank Justin ! :-)
On Fri, Jan 11, 2013 at 5:26 PM, Justin Lemkul wrote:
>
>
> On 1/10/13 11:37 PM, Kieu Thu Nguyen wrote:
>
>> Thank Justin and Peter so much !
>> Can i make a new box (it's size is not a multiples of the size of the
>> previous box) from a smaller lipid bilayer box ?
>>
>> I d
On 1/11/13 6:33 AM, Alexej Mazheika wrote:
Dear Justin,
The grompp doesn't show any fatal error. Using gmxdump I have checked the
topol.tpr file, and I found that C6 and C12 parameters of LJ have there
completely different values in contrast to those I wrote in silver.itp!
Maybe it is the reas
Dear Justin,
The grompp doesn't show any fatal error. Using gmxdump I have checked the
topol.tpr file, and I found that C6 and C12 parameters of LJ have there
completely different values in contrast to those I wrote in silver.itp!
Maybe it is the reason. But I wrote parameters in *.itp in units of
Hi all,
When calculating the average number of hbonds during a simulation, does the
program g_hbond contemplate the possibility of an atom involved in two
hbond?
If I visualize the structures with molden, setting the same cutoff
criterion for hbonding than g_hbond utilizes, I found out that some O
On 1/11/13 5:02 AM, Alexej Mazheika wrote:
Hello
I removed PBC and set space conditions as you recommended. I also modified
a bit the grompp.mdp (new version is below). However, it did not help to
prevent the scattering of silver atoms in all directions. The change of
parameters in LJ doesn't
On 1/11/13 4:55 AM, Subramaniam Boopathi wrote:
Hello All
I have created a nwe residue "NIC" in AMBER 03
Forcrfield and I have added corresponding data to the aminoacid.rtp In the
aminoacid.rtp, I have added all atoms topology information then I type the
command
On 1/10/13 11:37 PM, Kieu Thu Nguyen wrote:
Thank Justin and Peter so much !
Can i make a new box (it's size is not a multiples of the size of the
previous box) from a smaller lipid bilayer box ?
I don't see genconf -nbox can do that.
genbox -cs old_lipids.gro -box x y z -o new_lipids.gro
Hi,
If you're simulating in the gas-phase, how come you want implicit
solvent?
Erik
On Jan 11, 2013, at 5:07 AM, Sanku M wrote:
Hi,
I am trying to do implicit solvent simulation for a protein in gas-
phase. I have a few questions :
1) should I use sd integrator?
2) should I also use n
Hello
I removed PBC and set space conditions as you recommended. I also modified
a bit the grompp.mdp (new version is below). However, it did not help to
prevent the scattering of silver atoms in all directions. The change of
parameters in LJ doesn't influence on the final geometry. It seems, that
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