>
>
> Message: 1
> Date: Sun, 10 Feb 2013 21:32:15 + (WET)
> From: bapti...@itqb.unl.pt
> Subject: Re: [gmx-users] Reference structure for PCA.
> To: Discussion list for GROMACS users
> Message-ID:
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
Hello Antonio,
Thank you very m
Last question (I hope).
How can I choose the force constant?
Indeed for the version 4.5, the force constant is defined by the
option dihre_fc in the mdp input file. After this force is multiply by
kfac contained in the dihedral_sections in the topology file
Now this option is obsolete. The f
Hi Vivek,
If you use the g_covar option -ref, you not only use the reference
structure for fitting, you use it for calculating the deviations. Your
covariance matrix is built as:
S = 1/N sum (x - ref) (x - ref)'
If you leave out the option -ref then the average structure will be
used for the cov
Hello all,
I have an isopeptide bond (between Lys site chain and carboxyl terminal of
Gly) in my system and I defined this with specbond.dat and additional
residue types and I edited .rtp files using Amber ff. Although I have this
bond at the beginning (before pdb2gmx), it looks I need to add addi
Hello Justin.
Help would really be appreciated. And yes you are correct and i
thought the same. Initially I tried using opls_345B but it didn't
work. In fact if I use opls_345B it gives me an additional error.
Anyhow here are the relevant files.
topology file:
# [atoms]
15 ; nr type re
Hi,
S = 1/N sum (x - ref) (x - ref)'
or
S = 1/(N-1) sum (x - ref) (x - ref)'
N: the number of frames
Which one is right?
2013/2/12 Tsjerk Wassenaar
> Hi Vivek,
>
> If you use the g_covar option -ref, you not only use the reference
> structure for fitting, you use it for calculating the devi
On 2/12/13 6:19 AM, Abhishek Acharya wrote:
Hello Justin.
Help would really be appreciated. And yes you are correct and i
thought the same. Initially I tried using opls_345B but it didn't
work. In fact if I use opls_345B it gives me an additional error.
Anyhow here are the relevant files.
topol
On 2/12/13 3:30 AM, durdagis wrote:
Hello all,
I have an isopeptide bond (between Lys site chain and carboxyl terminal of
Gly) in my system and I defined this with specbond.dat and additional
residue types and I edited .rtp files using Amber ff. Although I have this
bond at the beginning (befo
On 2/12/13 1:12 AM, neeru sharma wrote:
Dear Gromacs Users,
I have simulated a system of protein-ion complex. As a part of the
analysis, I want to see whether there are any H-bonds or other interactions
between the active site residues and the water surrounding those residues.
I was trying to
Hey Ahmet,
1/(N-1) sum (x-mean)(x-mean)'
is the unbiased estimator of the true (population) covariance matrix,
provided the observations are mutually independent (!)
In most cases, N is quite large, so it doesn't actually matter, and
the eigenvectors and order (not size) of the eigenvalues are i
Justin, it's not the artifacts of visualization program. At the beginning
distance for isopeptide bond is 1.38 Angs (and it's defined at the
specbond.dat);
LYS NZ 1 GLY C 1 0.13LYQ GLQ
together with energy minimization this distance increases to around 3.0
Angs
On 2/12/13 8:37 AM, durdagis wrote:
Justin, it's not the artifacts of visualization program. At the beginning
distance for isopeptide bond is 1.38 Angs (and it's defined at the
specbond.dat);
LYS NZ 1 GLY C 1 0.13LYQ GLQ
together with energy minimization thi
Hello:
I am using Gromacs4.6 and I extract one of my frame into .gro file by
command:
trjconv_mpi -f md.xtc -s md.tpr -dump 25000 -o md.gro
I found that the velocity information was not present in this
25ns-md.gro file:
Generated by trjconv : Protein t= 25000.0
54178
1TYR N
On 2/12/13 9:17 AM, Albert wrote:
Hello:
I am using Gromacs4.6 and I extract one of my frame into .gro file by command:
trjconv_mpi -f md.xtc -s md.tpr -dump 25000 -o md.gro
I found that the velocity information was not present in this 25ns-md.gro file:
Velocities are not stored in .xtc
On 02/12/2013 03:19 PM, Justin Lemkul wrote:
Velocities are not stored in .xtc files. They are stored in .trr
files, if nstvout != 0 in the .mdp file.
-Justin
Hi Justin:
thanks for kind comments. I used the following settings and I didn't
generate .trr file:
nstxout= 0
On 2/12/13 9:25 AM, Albert wrote:
On 02/12/2013 03:19 PM, Justin Lemkul wrote:
Velocities are not stored in .xtc files. They are stored in .trr files, if
nstvout != 0 in the .mdp file.
-Justin
Hi Justin:
thanks for kind comments. I used the following settings and I didn't generate
.trr
On 02/12/2013 03:28 PM, Justin Lemkul wrote:
Extract it from the .cpt file that corresponds to that frame.
-Justin
thanks a lot for such helpful comments. I found that the md production
produced two .cpt file:
state.cpt
state_prev.cpt
I am not sure which one would be the one I need D
On 2/12/13 9:32 AM, Albert wrote:
On 02/12/2013 03:28 PM, Justin Lemkul wrote:
Extract it from the .cpt file that corresponds to that frame.
-Justin
thanks a lot for such helpful comments. I found that the md production produced
two .cpt file:
state.cpt
state_prev.cpt
I am not sure whic
On 02/12/2013 03:33 PM, Justin Lemkul wrote:
gmxcheck is your friend, as well as the wiki.
http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File
A checkpoint file is always written at the last step of the
simulation, which seems to be what you were asking for previously.
-Just
Hello:
I've got a question for setting of .mdp file for MD productions. The
.trr file is really huge if we are going to run longer MD simulations.
In this case, I usually only consider generate .xtc file, but the
velocity is missed for all steps except the last one.
So I am just wondering,
On 2/12/13 9:45 AM, Albert wrote:
Hello:
I've got a question for setting of .mdp file for MD productions. The .trr file
is really huge if we are going to run longer MD simulations. In this case, I
usually only consider generate .xtc file, but the velocity is missed for all
steps except the l
On 2/12/13 9:40 AM, Steven Neumann wrote:
Dear Gmx Users,
I know it is possible to combine windows with different spring
constants into the one PMF curve using g_wham.
Do I have to somehow tell g_wham that one or two windows have
different spring constants?
No, they are read from the .tpr
On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul wrote:
>
>
> On 2/12/13 9:40 AM, Steven Neumann wrote:
>>
>> Dear Gmx Users,
>>
>> I know it is possible to combine windows with different spring
>> constants into the one PMF curve using g_wham.
>>
>> Do I have to somehow tell g_wham that one or two
Dear Justin Thank you for your reply,
I have set the Restraint Along the Z Axis . as follows
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
i funct fcx fcy fcz
1 1 0 0 100
#endif
A
Hello all,
I am afraid that, after reading all the documentation I could find about
Coul-SR and LJ-SR, I still do not understand what these terms account for.
I am running a simulation of one single polymer chain in water. My values
for cut-off radious are rlist=rcoulomb=rvdw=1.5, I am using PME
On 2/12/13 11:29 AM, Kavyashree M wrote:
Dear Users,
How can intra-protein hydrophobic contacts be found
for a trajectory. Most of the mails regarding this in the
list is regarding hydrophobic contacts between chains
or ligand and protein. So kindly help.
Create a group of hydrophobic atoms
On 2/12/13 11:06 AM, escajarro wrote:
Hello all,
I am afraid that, after reading all the documentation I could find about
Coul-SR and LJ-SR, I still do not understand what these terms account for.
I am running a simulation of one single polymer chain in water. My values
for cut-off radious ar
On 2/12/13 9:57 AM, Steven Neumann wrote:
On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul wrote:
On 2/12/13 9:40 AM, Steven Neumann wrote:
Dear Gmx Users,
I know it is possible to combine windows with different spring
constants into the one PMF curve using g_wham.
Do I have to somehow te
On 2/12/13 10:29 AM, vidhya sankar wrote:
Dear Justin Thank you for your reply,
I have set the Restraint Along the Z Axis . as follows
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
i funct fcxfcyfcz
1
Hi,
I was performing a NPT calculation, and I got this error:
The Y-size of the box (6.002812) times the triclinic skew factor (1.00)
is smaller than the number of DD cells (6) times the smallest allowed cell
size (1.000605)
I also tried to change the number of processors but I got the same
On 2/12/13 5:24 PM, Sonia Aguilera wrote:
Hi,
I was performing a NPT calculation, and I got this error:
The Y-size of the box (6.002812) times the triclinic skew factor (1.00)
is smaller than the number of DD cells (6) times the smallest allowed cell
size (1.000605)
I also tried to chang
Thank you Justin,
So, your advice is not to perform the npt calculation and to run the md
after the nvt?
Thank you,
Sonia Aguilera
--
View this message in context:
http://gromacs.5086.n6.nabble.com/Error-The-Y-size-of-the-box-times-the-triclinic-skew-factor-is-smaller-than-the-number-of-DD
On 2/12/13 5:44 PM, Sonia Aguilera wrote:
Thank you Justin,
So, your advice is not to perform the npt calculation and to run the md
after the nvt?
A common mistake is to think that there is a "standard" protocol that one must
follow. While it is true that for the condensed phase, a common
Hello everybody, I'm trying to install Gromacs 4.6 in my Ubuntu 12.04
laptop. As I am not a a skilled user, I tried the Quick and Dirty
Installation, After following the instructions I obtained this message when
trying to execute GMXRC:
david@HAL-9000:~$ /usr/local/gromacs/bin/GMXRC
/usr/local/gro
On 2/12/13 9:24 PM, David Sáez wrote:
Hello everybody, I'm trying to install Gromacs 4.6 in my Ubuntu 12.04
laptop. As I am not a a skilled user, I tried the Quick and Dirty
Installation, After following the instructions I obtained this message when
trying to execute GMXRC:
david@HAL-9000:~$ /
Hi,
I am sorry if this topic is not relevant for GROMACS forum, but I hope
someone has faced the same problem before and could give me some advice...
I need to simulate a relatively short protein (170aa) in water. No
structures are available for it, so I used a Modeller web server to get
some. Un
Thanks for your answer Justin. I followed your advice:
When I type
*$ source /usr/local/gromacs/bin/GMXRC*
*$*
Nothing happened, the prompt returns normally and no action is executed. Do
you have any idea?
On Tue, Feb 12, 2013 at 11:27 PM, Justin Lemkul wrote:
>
>
> On 2/12/13 9:24 PM, David S
hi all,
i am trying to find the coordination number using the rdf between two chains
in the system .my box contains two polymer chains with water molecules.i know
integrating 4*pi*r*r*g(r)*rho between 0 to first minima of rdf will give
coordination number .the first minima value i took from the rdf
>
> On 2/12/13 1:12 AM, neeru sharma wrote:
> > Dear Gromacs Users,
> >
> >
> > I have simulated a system of protein-ion complex. As a part of the
> > analysis, I want to see whether there are any H-bonds or other
> interactions
> > between the active site residues and the water surrounding those
>
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