On 9/3/13 8:14 AM, Steven Neumann wrote:
Dear Gmx Users,
i wish I could restrain some ions in my system (NA). I tried to include it
in ions.itp:
[ moleculetype ]
; molnamenrexcl
NA1
#ifdef POSRES_NA
[ position_restraints ]
; atom type fx fy fz
1 1 1000
Dear Gmx Users,
i wish I could restrain some ions in my system (NA). I tried to include it
in ions.itp:
[ moleculetype ]
; molnamenrexcl
NA1
#ifdef POSRES_NA
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
#endif
But it does not work. Woul
On 4/17/13 7:39 AM, Wu Chaofu wrote:
Dear gmxers,
As is well-known, molecular dynamics can be implemented with position
restrained in gromacs. Now I want to ensure whether energy minimization can
also be performed with position restrained. Thanks for any reply to this
letter.
Sure, try it and
Dear gmxers,
As is well-known, molecular dynamics can be implemented with position
restrained in gromacs. Now I want to ensure whether energy minimization can
also be performed with position restrained. Thanks for any reply to this
letter.
Chaofu Wu
--
gmx-users mailing listgmx-users@gromacs.o
Hi Atila,
> ; Include chain topologies
> #include "complex_Protein_chain_A.itp"
> #include "complex_DNA_chain_B.itp"
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre_Protein_chain_A.itp"
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre_Protein_chain_B.
Atila Petrosian wrote:
Dear Justin
thanks for your attention
I deleted posre.itp file which pdb2gmx was created (containing all
solute).I made a posre.itp (containing only protein) by genrestr.
now if I use define = -DPOSRES, gromacs use from my posre.itp. is it true?
Assuming you have
On 27/10/2011 12:28 AM, Atila Petrosian wrote:
Dear Mark
thanks for your reply
you said "if pdb2gmx is able to treat the whole system in one pass,
then it will write such position restraint
files automatically"
in my system, what pdb2gmx includes are in below:
; Include forcefield parameter
Dear Justin
thanks for your attention
I deleted posre.itp file which pdb2gmx was created (containing all solute).I
made a posre.itp (containing only protein) by genrestr.
now if I use define = -DPOSRES, gromacs use from my posre.itp. is it true?
--
gmx-users mailing listgmx-users@gromacs.or
Atila Petrosian wrote:
I want to use define = -DPOSRES_Protein_chain_A for step 1.
is it true?
Not per the topology you posted earlier. Your only option (at this point) for
restraining the protein is -DPOSRES, which restrains all the chains.
If you want to restrain parts of your stru
I want to use define = -DPOSRES_Protein_chain_A for step 1.
is it true?
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Dear Mark
thanks for your reply
you said "if pdb2gmx is able to treat the whole system in one pass, then it
will write such position restraint
files automatically"
in my system, what pdb2gmx includes are in below:
; Include forcefield parameters
#include "amber03.ff/forcefield.itp"
; Include c
On 26/10/2011 11:24 PM, Atila Petrosian wrote:
Dear all
my system contains protein + ligand+ water molecules.
protein + ligand = solute
water molecules = solvent
I want to do minimization energy in 3 steps :
step 1) on protein only
step 2) on all solute (protein + ligand)
step 3) on all sy
Dear all
my system contains protein + ligand+ water molecules.
protein + ligand = solute
water molecules = solvent
I want to do minimization energy in 3 steps :
step 1) on protein only
step 2) on all solute (protein + ligand)
step 3) on all system
should I use position restrained minimizati
On 21/11/2010 4:01 AM, pawan raghav wrote:
Dear All,
Hope this mail will find you in good health.
I am facing a problem regarding Position restrained dynamics (PR). I
have done Molecular dynamic simulation
(for cytosolic protein) but has not performed PR. So i m little
confused if this effects
Dear All,
Hope this mail will find you in good health.
I am facing a problem regarding Position restrained dynamics (PR). I have
done Molecular dynamic simulation
(for cytosolic protein) but has not performed PR. So i m little confused if
this effects the results and if yes to what extent it effe
sunny mishra wrote:
Hi,
Thanks a lot for the quick reply. I want to position restrain the head
group atoms of CG DSPC but I am not sure about the head group molecules
in DSPC. Can you please tell me how to figure out the head group atoms
Presumably there is a structure of DSPC somewhere
Hi,
Thanks a lot for the quick reply. I want to position restrain the head group
atoms of CG DSPC but I am not sure about the head group molecules in DSPC.
Can you please tell me how to figure out the head group atoms or molecules.
Also, when you say co-ordinate file then you mean .itp file for t
sunny mishra wrote:
Dear All,
I am trying to run the Position Restrained simulation for the Coarse
Grained DSPC bi-layer. However, I am quite confused that how to generate
the position restraint file for the CG atoms in lipid. Is there a
difference between the position restraint file for th
Dear All,
I am trying to run the Position Restrained simulation for the Coarse Grained
DSPC bi-layer. However, I am quite confused that how to generate the
position restraint file for the CG atoms in lipid. Is there a difference
between the position restraint file for the fine grained and coarse g
nikhil damle wrote:
Hi All,
I am trying to simulate kinase domain (chain A) in complex with cyclin
(chain B). During solvent dynamics, PBC on and PME treatment of
electrostatics, i need to keep only kinase domain flexible but cyclin fixed.
i put POSRES_B in define variable and tried to sim
Hi All,
I am trying to simulate kinase domain (chain A) in complex with cyclin (chain
B). During solvent dynamics, PBC on and PME treatment of electrostatics, i need
to keep only kinase domain flexible but cyclin fixed.
i put POSRES_B in define variable and tried to simulated the entire solvat
Hi All,
I am trying to simulate kinase domain (chain A) in complex with cyclin (chain
B). During solvent dynamics, PBC on and PME treatment of electrostatics, i need
to keep only kinase domain flexible but cyclin fixed.
i put POSRES_B in define variable and tried to simulated the entire solvate
Dear All,
I am trying to do position restrained dynamics of a protein with
co-factor in Gromacs Version 4. But after running for a while (1390
steps), the run is simply stopping. I am not getting any message on
log file or terminal. Please help to identify the problem.
This is my pr.mdp file
Hi,
If we're really talking about timestepe here, then position restraints
have no impact as far as I know. If, on the other hand, we're talking
about total simulation time, then the size of your system will affect
the time required to relax the structure. In the end it depends on what
protei
Dear friends,
I am working to study dynamic behaviour of a protein molecule, having
3666 atoms. My question is related to position restrained dynamics
step.
What should be the time step in position restrained dynamics ?
This time i am giving 100ps, but i don't know is it sufficient to sock
the wat
Jayant James Jayasundar wrote:
Hello gmx-users!
1. Is it possible to perform position restrained energy minimisation?
Of course.
2. If so what are the parameter that I need to incorporate in the
em.mdp file. By just changing the
define = -DFLEX_SPC in the em.mdp to
make that
define = -DFL
Hello gmx-users!
1. Is it possible to perform position restrained energy minimisation?
2. If so what are the parameter that I need to incorporate in the em.mdp file. By just changing the
define = -DFLEX_SPC in the em.mdp to
define = -DPOSRES will it mean that I am now entering into position
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