Dear gmx users,
I used the NVT (T=300) equilibration for my system ( a protein in water). The
first time, I set 100 ps for system for equilibration, It resulted in RMSD=3.96
with an average temperature around 299.803 K.
Then I though of a better convergence, so set the equilibration to 200
: Thursday, August 09, 2012 1:23 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] NVT equilibration
Dear gmx users,
I used the NVT (T=300) equilibration for my system ( a protein in water). The
first time, I set 100 ps for system for equilibration, It resulted in RMSD=3.96
Parts of your system shifted too much (in Y dimension) for PME to handle.
What happens to the system up to the point of the crash?
How large is the system (particle count) vs. # of PME nodes used?
Could be your system is too small for the # of PME nodes used
Is the protein somehow interacting
?
Sincerely,
Shima
- Original Message -
From: Peter C. Lai p...@uab.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Thursday, August 9, 2012 5:08 PM
Subject: Re: [gmx-users] NVT equilibration
Parts of your system shifted too much (in Y dimension) for PME to handle
: Re: [gmx-users] NVT equilibration
Parts of your system shifted too much (in Y dimension) for PME to handle.
What happens to the system up to the point of the crash?
How large is the system (particle count) vs. # of PME nodes used?
Could be your system is too small for the # of PME nodes
Respected sir,
I am studying about micelle formation .. After setting box and adding
water i went for energy minimization and then went for nvt equilibration
for 1ns. when i visualized my nvt.pdb file, i found that my protein comes
together and formed three micelle like structure. but my box
On 16/05/2012 4:18 PM, priya thiyagarajan wrote:
Respected sir,
I am studying about micelle formation .. After setting box and adding
water i went for energy minimization and then went for nvt
equilibration for 1ns. when i visualized my nvt.pdb file, i found that
my protein comes together
Hi Priya,
My query is different than your problem ..
I wondered Is you use position restrained in nvt...??
In position restrained protein comes togather or you remove
position restraind ...
Sorry for trouble you...
With Best wishes,
Rama David
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Respected sir,
thanks for your kind reply...
i applied position restrain during nvt step sir..
Thanking you,
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Dear all
I'm studying a membrane protein. I've run equilibration with the follwing
parameters - reference temperature =323k
integrator = md ; leap-frog integrator
nsteps = 5 ; 2 * 5 = 100 ps
dt = 0.002 ; 2 fs
tcoupl = V-rescale ; modified Berendsen thermostat
The
Alex Jemulin wrote:
Dear all
I'm studying a membrane protein. I've run equilibration with the
follwing parameters - reference temperature =323k
integrator = md ; leap-frog integrator
nsteps = 5 ; 2 * 5 = 100 ps
dt = 0.002 ; 2 fs
tcoupl = V-rescale ; modified Berendsen thermostat
The
Dear all
I'm studying a membrane protein. I've run equilibration with the follwing
parameters - reference temperature =323k
integrator = md ; leap-frog integrator
nsteps = 5 ; 2 * 5 = 100 ps
dt = 0.002 ; 2 fs
tcoupl = V-rescale ; modified Berendsen thermostat
The
Hello Justin,
I am curious to know that why have nvt equilibration is not performed in
umbrella sampling?
Thanx.
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swati patel wrote:
Hello Justin,
I am curious to know that why have nvt equilibration is not performed in
umbrella sampling?
NVT is not necessarily required. I just happen to know that the system used in
the tutorial is rather robust and can proceed straight to NPT. Typically NVT is
*Dear All,
But I scaled the solvent box according to the density using
editconf_d command line. Then I carried out EM and NVT equilibration.*
*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.
+91-9686933963.*
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Ravi Kumar Venkatraman wrote:
*Dear All,
But I scaled the solvent box according to the density
using editconf_d command line. Then I carried out EM and NVT equilibration.*
Scaling the box with editconf simply scales the coordinates of the molecules in
it, which may or may
, 6 October 2011 9:35 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] NVT Equilibration
Ravi Kumar Venkatraman wrote:
*Dear All,
But I scaled the solvent box according to the density
using editconf_d command line. Then I carried out EM and NVT
Concur. I just used this approach to equilibrate a box of
water/acetonitrile. If your box shrinks too much, you can probably
use editconf and genbox to replicate the equilibrated box into a
larger box of arbitrary size and shape.
MZ
On Thu, Oct 6, 2011 at 4:36 PM, Dallas Warren
Dear All,
I downloaded ethanol.pdb file from prodrg server (all-atom). I
used ethanol.itp file that was in oplsaa.ff directory of gromacs to create
topology file for ethanol. I used genconf_d command to generate solvent box
of 512 molecules (as of Bevan's gromacs tutorial) and then I
On 5/10/2011 6:36 PM, Ravi Kumar Venkatraman wrote:
Dear All,
I downloaded ethanol.pdb file from prodrg server
(all-atom). I used ethanol.itp file that was in oplsaa.ff directory of
gromacs to create topology file for ethanol. I used genconf_d command
to generate solvent box of
Dear All,
My commands where,
genconf_d -f ethanol.gro -o ethanol512.gro -nbox 8 8 8
editconf_d -f eth512.gro -density 785.22 -o den.gro
I saw the den.gro by using VMD. I saw only as points but not the
molecules.
EM:
grompp_d -f em.mdp -c den.gro -p ethanol.top -o em.tpr
*Dear all,
I have been trying to generate pre-equilibrated ethanol solvent
box of 512 molecules in **OPLSAA ff. I used ethanol.itp in oplsaa.ff
directory for generating the topology file for ethanol. After NVT
equilibration some of the molecules get aggregated and there is some void
On 4/10/2011 6:16 PM, Ravi Kumar Venkatraman wrote:
*Dear all,
I have been trying to generate pre-equilibrated ethanol
solvent box of 512 molecules in **OPLSAA ff. I used ethanol.itp in
oplsaa.ff directory for generating the topology file for ethanol.
After NVT equilibration some
[mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Ravi Kumar Venkatraman
Sent: Tuesday, 4 October 2011 6:17 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] NVT equilibration of Ethanol in OPLSAA.
Dear all,
I have been trying to generate pre-equilibrated ethanol solvent
box of 512
Dear All,
I am doing NVT equilibration for Ethanol of cubic box of side
length 6.10346 nm in OPLSAA ff after doing the Energy Minimisation. My
system getting blown up when I do NVT equilibration.
Following are the some parameters that I have mentioned in *.mdp files,
100 ps run in 2
On 1/10/2011 5:09 PM, Ravi Kumar Venkatraman wrote:
Dear All,
I am doing NVT equilibration for Ethanol of cubic box of
side length 6.10346 nm in OPLSAA ff after doing the Energy
Minimisation. My system getting blown up when I do NVT equilibration.
Following are the some
Dear GROMACS users,
I have generated a 4*4*4 octahedral DMSO box containing 64 molecules (Charmm
all-atom force field) which need to be NVT equilibrated in order to pass it
for usage in genbox. Could one of you provide info on how to do the NVT and
periodic boundary equilibration to remove the
On 21/06/2011 2:44 AM, udaya kiran marelli wrote:
Dear GROMACS users,
I have generated a 4*4*4 octahedral DMSO box containing 64 molecules
(Charmm all-atom force field) which need to be NVT equilibrated in
order to pass it for usage in genbox. Could one of you provide info
on how to do the
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