Hi Dallas, Justin, e.a.,
As has been mentioned a number of times 0.9 +- 190 and 2.3 +- 190 are not
statistically different.
This is not true. Whether this is statistically different depends on the
number of independent samples. For pressure, the fluctuations are wild, and
the autocorrelation
I think you should add -tau 0 when using flooding as harmonic restraint
(since you do not want the flooding potential to change).
Okay, adding -tau 0 does turn it properly into a harmonic potential,
according to edsam.xvg. However, the average position of the resulting
(gaussian) is near but
On 9/11/13 11:33 PM, aixintiankong wrote:
i want to analyze the change of secondary structure of the mainchian frome
residue 20 to residue 60. so i want to make a index file that only contain
the maninchian+H from residue 20 to residue 60. i have inputed the command
make_ndx -f em.pdb -o
Hi
[ bondedtypes ]
; Col 1: Type of bond
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
; Col 4: Type of improper dihedrals
; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
; Col 6: Number of excluded neighbors for nonbonded interactions
; Col 7: Generate 1,4 interactions
On 9/12/13 9:21 AM, Rama Krishna Koppisetti wrote:
Hi
[ bondedtypes ]
; Col 1: Type of bond
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
; Col 4: Type of improper dihedrals
; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.
; Col 6: Number of excluded neighbors for
Dear GMX users,
I'd like to perform the umbrella sampling using the pull codes in gromacs.
The reaction coordinate is defined as the distance between the center of mass
(DCOM) of two domains in a protein. The following script is used:
--- only for pull section
; Pull code
On 9/12/13 9:55 AM, mjyang wrote:
Dear GMX users,
I'd like to perform the umbrella sampling using the pull codes in gromacs.
The reaction coordinate is defined as the distance between the center of mass
(DCOM) of two domains in a protein. The following script is used:
Hi,
These are the parameters I kept in the .rtp file for DMPC molecule. Still
getting same error message should I need to look at somewhere else.
[ bondedtypes ]
; Col 1: Type of bond
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
; Col 4: Type of improper dihedrals
; Col 5: Generate
On 9/12/13 1:17 PM, Rama Krishna Koppisetti wrote:
1. Did you re-run pdb2gmx after modifying the .rtp file?
Yes.. I do run with modified .rtp file but output was same as previous.
2. Have you looked into the [bonds] directive in the .top file that pdb2gmx
created to see if anything is out of
1. Did you re-run pdb2gmx after modifying the .rtp file?
Yes.. I do run with modified .rtp file but output was same as previous.
2. Have you looked into the [bonds] directive in the .top file that pdb2gmx
created to see if anything is out of place? Every line should have 5
entries:
[bonds]
On 9/12/13 2:57 PM, Rama Krishna Koppisetti wrote:
Hi Justin,
Output topology from pdb2gmx. You could see some entries differ between
two molecules.
I'm looking forward to do restrained MD for this system by using Gromacs.
[ moleculetype ]
; Namenrexcl
Protein 3
[
Hi Justin,
Output topology from pdb2gmx. You could see some entries differ between
two molecules.
I'm looking forward to do restrained MD for this system by using Gromacs.
[ moleculetype ]
; Namenrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr
On 9/12/13 11:03 AM, Rama Krishna Koppisetti wrote:
Hi,
These are the parameters I kept in the .rtp file for DMPC molecule. Still
getting same error message should I need to look at somewhere else.
[ bondedtypes ]
; Col 1: Type of bond
; Col 2: Type of angles
; Col 3: Type of proper dihedrals
I carried out independent NPT processes with different tau_p values =
1.5,
1.0 and 0.5
## tau_p 1.5
Energy Average Err.Est. RMSD Tot-Drift
---
Pressure2.62859
I see,
when you say thorough parametrization and validation, what do you mean?
How does one validate the system, calculate free energy in solution and
compare it to tabulated data?
On Wed, Sep 11, 2013 at 4:57 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/11/13 6:07 PM, Rafael I. Silverman
Dear Justin,
Thanks for your reply. I checked the content in pullx.xvg file as follows:
# GRowing Old MAkes el Chrono Sweat
#
@title Pull COM
@xaxis label Time (ps)
@yaxis label Position (nm)
@TYPE xy
@ view 0.15, 0.15, 0.75,
On 9/12/13 6:37 PM, Dwey Kauffman wrote:
I carried out independent NPT processes with different tau_p values =
1.5,
1.0 and 0.5
## tau_p 1.5
Energy Average Err.Est. RMSD Tot-Drift
---
On 9/12/13 7:04 PM, Rafael I. Silverman y de la Vega wrote:
I see,
when you say thorough parametrization and validation, what do you mean?
How does one validate the system, calculate free energy in solution and
compare it to tabulated data?
The target data depend on the force field for
On 9/12/13 10:18 PM, mjyang wrote:
Dear Justin,
Thanks for your reply. I checked the content in pullx.xvg file as follows:
# GRowing Old MAkes el Chrono Sweat
#
@title Pull COM
@xaxis label Time (ps)
@yaxis label Position
Dear Justin,
What is the meaning of the minus number for the distance in the 3rd
column? Does it mean that the moving group is at the minus direction wrt the
reference group along Z?
Many thanks.
Mingjun
From: gmx-users-boun...@gromacs.org
On 9/12/13 10:41 PM, mjyang wrote:
Dear Justin,
What is the meaning of the minus number for the distance in the 3rd
column? Does it mean that the moving group is at the minus direction wrt the reference
group along Z?
Yes, since it is a vector quantity. The positions should be very
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