Hello,
I am trying to run a simulation for flexiable water. I use the parameters
from J. Chem. Phys. (2006),124,024503 paper and made floowing changes.
I addes "WAT" as a new residue name in aminoacids.dat
I addred two atom times in ffoplsaa.atp
opls_1001 15.99940 ; O SPC_fw Water
opls_100
Dear gmx user,
i wanted to simulate cooperativity effect of
heamoglobin through steered MD for that i need to pull oxygen molecule at the
same time Fe atom of phorphyrin ring (protruding above the plane of Phorphyrin
ring in the initial PDB) should go to the plane of pho
Nilesh Dhumal wrote:
Hello,
I am trying to run a simulation for flexiable water. I use the parameters
from J. Chem. Phys. (2006),124,024503 paper and made floowing changes.
I addes "WAT" as a new residue name in aminoacids.dat
I addred two atom times in ffoplsaa.atp
opls_1001 15.99940 ;
I have total 256 water molecules. I am trying to genrate the .top file
from .pdb so I used pdb2gmx.
How can I genrate the .top file with pdb2gmx for 256 water molecules.
Nilesh
On Tue, April 26, 2011 1:01 pm, Justin A. Lemkul wrote:
>
>
> Nilesh Dhumal wrote:
>
>> Hello,
>>
>>
>> I am trying t
Nilesh Dhumal wrote:
I have total 256 water molecules. I am trying to genrate the .top file
from .pdb so I used pdb2gmx.
pdb2gmx is only really useful for building topologies for linear molecules built
from repeat building blocks, not for systems of individual molecules.
How can I genra
Hi, gromacs developers,
It seems that there is a bug regarding the angular moment removal.
This may not be very important for many users since most of them are
doing PBC where it is irrelevant, but if you are doing cluster or if you
really care the angular momentum like I
do(I want the ang
Dear gmx users,
I need to design a starting configuration of a polypeptide with charged side
chains sitting in a box of water with Cl- ions within 7 ang of its radius.
I realize that in such a system like charges will essentially prefer to be
as far as possible from each other, but I still need t
Dear Gromacs users
I ahve a dppc monolayer on water layer 9tip4p-2005). I have added 8 Mg and 16
Cl ions using genion and now want to use grompp and then start the simulation
to see the effect of ions on the pressure-area isotherm of the system.
running grompp in gromacs 3.3 I see he following
delara aghaie wrote:
Dear Gromacs users
I ahve a dppc monolayer on water layer 9tip4p-2005). I have added 8 Mg
and 16 Cl ions using genion and now want to use grompp and then start
the simulation to see the effect of ions on the pressure-area isotherm
of the system.
running grompp in groma
Dear gmx-users,
I intended to concantanate two trajectories with no similar time frames
i.e., both files have distinct time frames. But once I combine the files
many time frames are skipped, details are as follows:
File 1 has 2175 frames
File 2 has 1232 frames
I used the following command to con
Lipi Thukral wrote:
Dear gmx-users,
I intended to concantanate two trajectories with no similar time frames
i.e., both files have distinct time frames. But once I combine the files
many time frames are skipped, details are as follows:
File 1 has 2175 frames
File 2 has 1232 frames
What d
I got the same error when doing the lysozyme tutorial on one of the machines
provided by NERSC.
the dept. of energy provided high performance computing service, specifically
the carver machine.
The gromacs default on that machine I think is also 3.*.*, so I'll go with the
"former" also, namel
Hi,
I am trying to write a topology in gromacs format for a recently developed
molecule in OPLS format. From the parameterization-paper, I know the partial
charges on each of the atom in that molecule from the corresponding paper .
But,
I am not sure how to split the molecule topology into se
Sanku M wrote:
Hi,
I am trying to write a topology in gromacs format for a recently
developed molecule in OPLS format. From the parameterization-paper, I
know the partial charges on each of the atom in that molecule from the
corresponding paper . But, I am not sure how to split the molecul
On 4/27/2011 1:29 AM, Nilesh Dhumal wrote:
Hello,
I am trying to run a simulation for flexiable water. I use the parameters
from J. Chem. Phys. (2006),124,024503 paper and made floowing changes.
I addes "WAT" as a new residue name in aminoacids.dat
I addred two atom times in ffoplsaa.atp
op
On 4/27/2011 6:21 AM, delara aghaie wrote:
Dear Gromacs users
I ahve a dppc monolayer on water layer 9tip4p-2005). I have added 8 Mg
and 16 Cl ions using genion and now want to use grompp and then start
the simulation to see the effect of ions on the pressure-area isotherm
of the system.
runn
On 4/27/2011 5:13 AM, shivangi nangia wrote:
Dear gmx users,
I need to design a starting configuration of a polypeptide with
charged side chains sitting in a box of water with Cl- ions within 7
ang of its radius.
I realize that in such a system like charges will essentially prefer
to be as
Hi gromacs experts,
I used gromacs 4.5.3. my system has only spce water, no other types.
In .mdp file,
I used the following parameters;
define =
constraints = none
constraint-algorithm = Lincs
Can u tell me Is it flexible water or all the bond, angle fixed using the
above setting?
MD wrote:
Hi gromacs experts,
I used gromacs 4.5.3. my system has only spce water, no other types.
In .mdp file,
I used the following parameters;
define =
constraints = none
constraint-algorithm = Lincs
Can u tell me Is it flexible water or all the bond, angle fixed using
the abo
Hi Justin,
When i define
define = FLEXIBLE
constraints = none
constraint-algorithm = Lincs
I saw my .log file.
Input Parameters:
integrator = md
nsteps = 1
init_step= 0
ns_type = Grid
nstlist = 5
ndelta
On 4/27/2011 11:52 AM, MD wrote:
Hi Justin,
When i define
define = FLEXIBLE
This is not of the correct form.
constraints = none
constraint-algorithm = Lincs
I saw my .log file.
Input Parameters:
integrator = md
nsteps = 1
init_step = 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstco
Hello dear user,
after 5ns MD,I used trjconv -f -s -pbc -mol -center -o *.pdb command to get
the whole protein without any separation,but I found some part of the residue
was broken,and some new bond at the end of some residue was formed.I need the
intact molecule for docking,but how should I
The Urey Bradley constant in CHARMM is expressed in units of kcal per (mol
squared angstrom). However, in the Gromacs manual in Table 5.5, it is expressed
in kJ/mol. How do we convert the constant from kcal per (mol squared angstrom)
to kJ/mol in gromacs. Could gromacs have been expressing this
Hi Justin,
I am using Gromacs 4.5 beta-2.
gmxcheck with file 1 and file 2 tells me exactly the number of frames I
specified.
gmxcheck -f File1.xtc
Frames: 2175
gmxcheck -f File2.xtc
Frames: 1232
While after concatenating, it skips the frames and the combined trajectory
results in 1266 frames.
Do
On 2011-04-26 19.38, Xiaohu Li wrote:
Hi, gromacs developers,
It seems that there is a bug regarding the angular moment removal. This
may not be very important for many users since most of them are doing
PBC where it is irrelevant, but if you are doing cluster or if you
really care the angular mo
On 2011-04-27 07.51, Lipi Thukral wrote:
Hi Justin,
I am using Gromacs 4.5 beta-2.
gmxcheck with file 1 and file 2 tells me exactly the number of frames I
specified.
gmxcheck -f File1.xtc
Frames: 2175
gmxcheck -f File2.xtc
Frames: 1232
While after concatenating, it skips the frames and the com
Dear All
How can I get a list of all articles which have used Gromacs Package for
their work?
I looked at citations for 4 principal papers in gromacs website,but most of
them were not simulations but
improving algorithms such as lincs and etc.
Some packages as Lammps saves articles which use lam
On 4/27/2011 3:16 PM, Mr Bernard Ramos wrote:
The Urey Bradley constant in CHARMM is expressed in units of kcal per
(mol squared angstrom). However, in the Gromacs manual in Table 5.5,
it is expressed in kJ/mol. How do we convert the constant from kcal
per (mol squared angstrom) to kJ/mol in gr
On 2011-04-27 08.49, mohsen ramezanpour wrote:
Dear All
How can I get a list of all articles which have used Gromacs Package for
their work?
I looked at citations for 4 principal papers in gromacs website,but most
of them were not simulations but
improving algorithms such as lincs and etc.
Ther
dear justin,
Hello,after 5ns MD,based on your recommend, I use" trjconv -f -s -pbc -mol
-center -o *.pdb" command to get the whole protein without any separation,but I
found some part of the residue was broken,and some new bond at the end of some
residue was formed.I need the intact molecule f
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