Hi,
happy diwali to you, too.
Can you please post a link where what you said is stated?
it seems quite strange to me!
2012/11/12 Venkat Reddy venkat...@gmail.com
Dear gromacs users,
I have a very basic doubt regarding mdrun. Is there any difference between
doing final MD for 100 ns at a
Hello,
do_dssp (4.5.5) is broken. There are two possible answers you're gonna get
here:
1) Use old dssp, which you are using.
2) You're an idiot, which are not.
What I did to solve the problem was, download gmx from git, and substitute
the /src/tools/do_dssp.c of gmx 4.5.5 with the one from the
Hi Francesco,
Thanks for ur reply and wishes. I couldn't remember exactly where I read
this but what is your opinion on this discrete vs continuous runs ?
On Mon, Nov 12, 2012 at 2:10 PM, francesco oteri
francesco.ot...@gmail.comwrote:
Hi,
happy diwali to you, too.
Can you please post a link
Thank you for your reply.
On Sun, Nov 11, 2012 at 8:30 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/11/12 4:51 AM, rama david wrote:
Hi justin ,
Thank you a lot for your explaination.
My opinion on the working of g_mindist -pi is that when it shows the
distance between two atom
of
Dear Justin,
Thank you for your previous reply,
I
am doing Protein-Lipid simulation. After Em When I visualize the str in .vmd
The water Molecules Present in Lipid (DPPC) Head groups .There is No
Hi,
The explanation is that DSSP changed its syntax some time ago and do_dssp no
longer complied. More recent versions of do_dssp follows the new syntax while
still supporting the old one.
Erik
12 nov 2012 kl. 10.55 skrev João Henriques:
Hello,
do_dssp (4.5.5) is broken. There are two
Ok, what i've currently done:
I start with a pdb file of a single molecule Lipid_A and its topology and
put it in a box:
editconf -f Lipid_A.pdb -o Lipid_A-box.gro -bt triclinic -d 1.0
I want a total of 128 molecules of this lipid in my system so I use genbox
to add 127 more:
genbox -cp
Dear Gromacs users,
How to launch mdrun_mpi using g_tune_pme on a cluster, because
*
*
*g_tune_pme -launch *launches mdrun but not mdrun_mpi.
Thanks for your valuable time
--
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
On 11/12/12 7:40 AM, Venkat Reddy wrote:
Dear Gromacs users,
How to launch mdrun_mpi using g_tune_pme on a cluster, because
*
*
*g_tune_pme -launch *launches mdrun but not mdrun_mpi.
Thanks for your valuable time
Please read g_tune_pme -h, which describes how you can set the names of
On 11/12/12 6:35 AM, vidhya sankar wrote:
Dear Justin,
Thank you for your previous reply,
I
am doing Protein-Lipid simulation. After Em When I visualize the str in .vmd
The water Molecules
On 11/12/12 7:03 AM, jonas87 wrote:
Ok, what i've currently done:
I start with a pdb file of a single molecule Lipid_A and its topology and
put it in a box:
editconf -f Lipid_A.pdb -o Lipid_A-box.gro -bt triclinic -d 1.0
I want a total of 128 molecules of this lipid in my system so I use
Dear GROMACS user,
I am running in major problems trying to use gromacs 4.6 on my desktop
with two GTX 670 GPU's and one i7 cpu. On the system I installed the
CUDA 4.2, running fine for many different test programs.
Compiling the git version of gromacs 4.6 with hybrid acceleration I get
one error
Hello:
Recently, in a released paper I found that some one claimed they've
observed a Asp is protonated and deprotonated from time to time during a
micro second MD simulation by Gromacs. I am still curious about such
kind of observation. Does anybody else observe a covalent bond can be
Dear GMX users
Hi. I'm calculating some small organic molecule's desolvation free energy.
Recently i got this error from BAR calculation. Please anyone explain what's
wrong in here?
First:
WARNING: Using the derivative data (dH/dlambda) to extrapolate delta H values.
This will only work if
Dear all,
i did some scaling tests for a cluster and i'm a little bit clueless
about the results.
So first the setup:
Cluster:
Saxonid 6100, Opteron 6272 16C 2.100GHz, Infiniband QDR
GROMACS version: 4.0.7 and 4.5.5
Compiler: GCC 4.7.0
MPI: Intel MPI 4.0.3.008
FFT-library: ACML 5.1.0
On 11/12/12 10:29 AM, Albert wrote:
Hello:
Recently, in a released paper I found that some one claimed they've observed a
Asp is protonated and deprotonated from time to time during a micro second MD
simulation by Gromacs. I am still curious about such kind of observation. Does
anybody else
Hi Thomas,
On Nov 12, 2012, at 5:18 PM, Thomas Schlesier schl...@uni-mainz.de wrote:
Dear all,
i did some scaling tests for a cluster and i'm a little bit clueless about
the results.
So first the setup:
Cluster:
Saxonid 6100, Opteron 6272 16C 2.100GHz, Infiniband QDR
GROMACS version:
On 11/12/2012 04:12 PM, sebastian wrote:
Dear GROMACS user,
I am running in major problems trying to use gromacs 4.6 on my desktop
with two GTX 670 GPU's and one i7 cpu. On the system I installed the
CUDA 4.2, running fine for many different test programs.
Compiling the git version of
Dear Users,
I would like to study water - TFE mixtures at different molar ratios.
Is it a reasonably approach to set the compressibility to the value of
water at [100/0 - water/TFE] and to that of tfe at [0/100 - water/TFE]
and scale the compressibility values for the other mixtures?
Thnak
Hi Sebastian,
That is very likely a bug so I'd appreciate if you could provide a bit more
information, like:
- OS, compiler
- results of runs with the following configurations:
- mdrun -nb cpu (to run CPU-only with Verlet scheme)
- GMX_EMULATE_GPU=1 mdrun -nb gpu (to run GPU emulation using
The simple answer is yes, you could make Lipid_A-box.gro larger in the bilayer
plane. That probably won`t
address the underlying problem though.
As far as I know, genbox doesn't take periodicity into account. That means that
with larger species, such as lipid A
you are going to need to start
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