Hi All,
when I run energy minimization the system gives error, and broke up. it has
error about steep integrator and says tha: "steepest time is too small".
but the system is running by MD integrator without any em step). is the energy
minimization necessary to all cases? for example in DL_POL
Szilárd ,
thanks again for explanation!
Today I've performed some tests on my calmodulin in water system with
different cutt-offs (I've used all cutt-ooffs 1.0 , 0.9 and 0.8
respectually)
Below you can see that the highest performance was in case of 0.8 cut-offs
all cut-offs 1.0
Force evaluat
Hi Boopathi,
Adding hydrogen atoms to the hdb is explained in the sectio 5.6.4 of
gromacs manual 4.5.4. Please refer the manual.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Thu, Jan 10, 2013 at 11:32 AM, Subramaniam Boopathi <
boopathi...@gmail.com> wrote:
> Dear All
>
>
>
thank you Justin.Now it is fine.
> --
>
> Message: 1
> Date: Wed, 9 Jan 2013 22:50:13 +0530
> From: SANTU BISWAS
> Subject: [gmx-users] energy-mimisation-problem
> To: gmx-users@gromacs.org
> Message-ID:
>
> Content-Type
Hi James,
The build looks mostly fine except that you are using fftw3 compiled with
AVX which is slower than with only SSE (even on AVX-capable CPUs) - you
should have been warned about this at configure-time.
Now, performance-wise everything looks fine except that with a 1.2 nm
cut-off your GPU
@ Justin,
Thank you, that worked like a charm! (Using increased vanderwal distance)
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 9, 2013, at 8:42 PM, Xu Dong Huang wrote:
> Everytime I remove the atom that is causing the INF
On 1/9/13 8:42 PM, Xu Dong Huang wrote:
Everytime I remove the atom that is causing the INF force, it gives me new atom
that causes INF force. (The ones that come up are all water beads that are causing
the infinite force), does that mean when i did genbox it inserted water
incorrectly? (Bec
Everytime I remove the atom that is causing the INF force, it gives me new atom
that causes INF force. (The ones that come up are all water beads that are
causing the infinite force), does that mean when i did genbox it inserted water
incorrectly? (Because I viewed it in VMD< it's certainly not
Dear users,
Now I fixed the initial structure error, and I solvated it in water (martini
bead model), and i run typical EM, I get the following error:
Steepest Descents:
Tolerance (Fmax) = 1.0e+01
Number of steps=5
Step= 14, Dmax= 1.2e-06 nm, Epot= 4.48322e+19 Fm
Must be something wrong with my editor program (BBEdit), because when I open
the file you sent me, it shows me there an additional blank line. Ok, time to
switch to regular text editor…
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
O
On 1/9/13 8:02 PM, Xu Dong Huang wrote:
Oh, you have an Additional line after vector size box…. I thought you said to
remove that blank line
There is no additional line. The last line in the file must be the box vectors.
-Justin
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers S
Oh, you have an Additional line after vector size box…. I thought you said to
remove that blank line
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 9, 2013, at 7:58 PM, Xu Dong Huang wrote:
> @Justin,
>
> I did that, and it sti
On 1/9/13 7:58 PM, Xu Dong Huang wrote:
@Justin,
I did that, and it still says I have 103.
I will send you a fixed file off-list so you can compare with what you've got.
I don't know what text editor you're using, but I can produce a correct file
using two different methods in vi. It's v
@Justin,
I did that, and it still says I have 103.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 9, 2013, at 7:49 PM, Xu Dong Huang wrote:
> @Justin,
>
> I did what you suggested, and I still can't load my molecule in VMD. Ma
On 1/9/13 7:49 PM, Xu Dong Huang wrote:
@Justin,
I did what you suggested, and I still can't load my molecule in VMD. Maybe I am
still doing something wrong with the new line character thing.
Go to the last line and go to the end of it. Hit enter. Hit backspace (brings
you back up to th
@Justin,
I did what you suggested, and I still can't load my molecule in VMD. Maybe I am
still doing something wrong with the new line character thing.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 9, 2013, at 7:22 PM, Xu Dong
@ Justin,
I laughed. :) Thank you. I can't believe I miss the smallest and most
rudimentary things.
Thanks again,
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 9, 2013, at 7:20 PM, Justin Lemkul wrote:
>
>
> On 1/9/13 7:16 P
On 1/9/13 7:16 PM, Xu Dong Huang wrote:
@ Justin,
Thanks for always saving me from my mistakes. But I don't quite understand what
is a new line character?
The thing you get when you press enter.
http://en.wikipedia.org/wiki/Newline#In_programming_languages
Note that Google has plenty mor
@ Justin,
Thanks for always saving me from my mistakes. But I don't quite understand what
is a new line character?
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 9, 2013, at 7:12 PM, Justin Lemkul wrote:
>
>
> On 1/9/13 7:07
On 1/9/13 7:07 PM, Xu Dong Huang wrote:
Dear all,
I created this .gro file following the gromacs format. But when I load it into
VMD, it doesn't show the structure or molecule, and I have made many .gro
before this one, and learned from many mistakes, but for this one, I don't know
what I d
Dear all,
I created this .gro file following the gromacs format. But when I load it into
VMD, it doesn't show the structure or molecule, and I have made many .gro
before this one, and learned from many mistakes, but for this one, I don't know
what I did wrong. I still proceeded to do simulatio
Hi,
is this an implicit water calculation? If so it shouldn't use PME.
Roland
On Wed, Jan 9, 2013 at 2:27 PM, James Starlight wrote:
> Dear Szilárd, thanks for help again!
>
> 2013/1/9 Szilárd Páll :
>
> >
> > There could be, but I/we can't well without more information on what and
> > how you
Dear Szilárd, thanks for help again!
2013/1/9 Szilárd Páll :
>
> There could be, but I/we can't well without more information on what and
> how you compiled and ran. The minimum we need is a log file.
>
I've compilated gromacs 4.6-3 beta via simple
cmake CMakeLists.txt -DGMX_GPU=ON -DCUDA_TOOLK
On 2013-01-09 12:25, Maria Astón Serrano wrote:
Hello,
I am new at this and I am working with the constraints algorithms used in a
MD simulation. I would like to now how they work, what type of coordinates
they use and also to identify some variables.
For that, I am trying to do a simulation wi
Dear James,
On Wed, Jan 9, 2013 at 6:17 PM, James Starlight wrote:
> Roland,
>
> indeed the error was that I'have compilate mdrun-openmm which is not
> the native gpu.
>
> now I've made mdrun via
>
> cmake CMakeLists.txt -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0
>
> and obtain wo
On Wed, Jan 9, 2013 at 10:27 AM, James Starlight wrote:
> I've solved previous problem but havent been able to launch
> mdrun-openmm. Below you can find mdrun's output
>
> Back Off! I just backed up md_test.log to ./#md_test.log.3#
> Reading file md_test.tpr, VERSION 4.6-beta3 (single precision)
>
On Wed, Jan 9, 2013 at 9:17 AM, James Starlight wrote:
> As I understood that gromacs version already has included openMM so
> the installation of the external openMM sources is not needed, isnt it
> ?
>
The manual and wiki guides are meant to be read. Although they are a bit
dated, the main body
Roland,
indeed the error was that I'have compilate mdrun-openmm which is not
the native gpu.
now I've made mdrun via
cmake CMakeLists.txt -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0
and obtain workable gromacs.
My test system consist of calmodulin (charmm27) solvated in tip3p
wate
On 1/9/13 12:20 PM, SANTU BISWAS wrote:
dear users,
I am performing an energy minimization of
apolypeptide(formed by alanine-10-residues) in vacuum box by using
Steepest Descent(initially) and then Conjugate Gradient methods in
gromacs_4.5.5_doubleprecision.The chain length of
a
look through the answer on my repost today. Maybe we can do it together?
--
View this message in context:
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--
gmx-users mailing listgmx-users@g
Thank you very much! A lot of users will thank you!
--
View this message in context:
http://gromacs.5086.n6.nabble.com/repost-hybrid-imlicit-explicit-solvent-tp5004383p5004397.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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gmx-users mailing listgmx-users@g
On 1/9/13 10:54 AM, Roland Schulz wrote:
Hi,
it seems you are using OpenMM. The recommended approach is to compile with
GMX_OPENMM=off and GMX_GPU=on.
...with version 4.6beta3.
The version shown is an outdated development version from the 4.5.1 era. OpenMM
was the only choice at that poi
Hi,
it seems you are using OpenMM. The recommended approach is to compile with
GMX_OPENMM=off and GMX_GPU=on.
Roland
On Wed, Jan 9, 2013 at 10:45 AM, sdlonga wrote:
> Hi,
>
> I succesfully built the mdrun-gpu on a MacOS MountainLion having one CUDA
> NVIDIA GeForce GTX 660 platform. When I tr
On Wed, Jan 9, 2013 at 3:17 AM, James Starlight wrote:
> As I understood that gromacs version already has included openMM so
> the installation of the external openMM sources is not needed, isnt it
> ?
>
No the new build in GPU implementation and openMM are two different things.
The Gromacs-OpenM
Hi,
I succesfully built the mdrun-gpu on a MacOS MountainLion having one CUDA
NVIDIA GeForce GTX 660 platform. When I try to run one of the GPU benchmarks
(e.g. dhfr-impl-1nm.bench) a floating point exception occurs. The same
happens for all the benchmarks. I have already tested the functionality
Dear GMX users,
I just wanted to know that it's possible one estimates Gibbs free
energy of evaporation via following the solvation free energy scheme?
I'm trying to obtain evaporation rate with using the value of G(evap.)
for different hydrocarbon molecules at different temperatures.
Any advice
>
>
> Hi all,
> I ran energy minimization (em) step, (protein-CNT in water) by these
> conditions:
> title = Minimization
> integrator = steep
> emtol = 1000.0
> emstep = 0.01
> nsteps = 15
> energygrps = Protein CNT
> nstlist = 1
> ns_typ
On 1/9/13 6:25 AM, Maria Astón Serrano wrote:
Hello,
I am new at this and I am working with the constraints algorithms used in a
MD simulation. I would like to now how they work, what type of coordinates
they use and also to identify some variables.
For that, I am trying to do a simulation wi
On 1/9/13 8:57 AM, sara azhari wrote:
Dear Justin
first ,I get error on atom number .
after change emtol to 10 , I get same error on atom number .
what' your idea? how to solve it?
mdrun probably did a different number of steps and/or moved through
configurations different.
Dear Justin
first ,I get error on atom number .
after change emtol to 10 , I get same error on atom number .
what' your idea? how to solve it?
I use this file for PR step , but I get this error:
A charge group moved too far between two domain decomposition
your system mig
On 1/9/13 6:02 AM, Алексей Раевский wrote:
Hi this is a repost, maybe it was missed.
I want to create a system with hybrid solvent (explicit/implicit). My
system is large enough to calculate it with explicit SOL. But it is
critical to study the behavior of several water molecules in the site.
Hello,
I am new at this and I am working with the constraints algorithms used in a
MD simulation. I would like to now how they work, what type of coordinates
they use and also to identify some variables.
For that, I am trying to do a simulation with a toy input system, like
methane or ethane but
Hi this is a repost, maybe it was missed.
I want to create a system with hybrid solvent (explicit/implicit). My
system is large enough to calculate it with explicit SOL. But it is
critical to study the behavior of several water molecules in the site. The
idea is to generate a layer of explicit wat
On 1/9/13 2:48 AM, 라지브간디 wrote:
Could you tell me which force field recognizes the GPI ligand which posses
lipid and mannose which interacts with protein?
Probably none do by default, but suitable parameters may exist within the
literature or with a Google search.
-Justin
--
===
On 1/9/13 3:41 AM, Gmx Niki wrote:
Hi all,
I ran energy minimization (em) step, (protein-CNT in water) by these conditions:
title= Minimization
integrator= steep
emtol= 1000.0
emstep = 0.01
nsteps= 15
energygrps= Protein CNT
nstlist= 1
ns_typ
I've solved previous problem but havent been able to launch
mdrun-openmm. Below you can find mdrun's output
Back Off! I just backed up md_test.log to ./#md_test.log.3#
Reading file md_test.tpr, VERSION 4.6-beta3 (single precision)
Changing nstlist from 10 to 40, rlist from 1 to 1.146
Compiled acc
Hi all,
I ran energy minimization (em) step, (protein-CNT in water) by these conditions:
title = Minimization
integrator = steep
emtol = 1000.0
emstep = 0.01
nsteps = 15
energygrps = Protein CNT
nstlist = 1
As I understood that gromacs version already has included openMM so
the installation of the external openMM sources is not needed, isnt it
?
also I wounder to know what exactly CUDA version is needed ? For
example I've tried lattest cuda-5.0 but with that version i've obtain
error from mdrun-openm
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