Dear Riccardo Concu,
The reason is that I used the make_ndx file in the working directory.
Now, I solved that problem with installing gromacs as following
cmake .. -DGMX_BUILD_OWN_FFTW=Off
Anyway, I appreciate your comment.
Best regards,
Changwoon Jang
On Friday, November 8, 2013
Dear Changwoon,
why are you using ./make_ndx instead of make_ndx? Did you try to use the
command without ./?
Regards
El jue, 07-11-2013 a las 14:12 -0800, Chang Woon Jang escribió:
> Dear Users,
>
> I am using openSUSE 12.3 and try to use make_ndx and g_angle. When I try
> the following com
Dear Users,
I am using openSUSE 12.3 and try to use make_ndx and g_angle. When I try
the following command, there is an error message.
> ./make.ndx -f data.pdb
./make_ndx: error while loading shared libraries: libcudart.so.4:cannot open
shared object file: No such file or directory
Do
OPLS-AA was generally derived with Monte Carlo, which means that all
bonds were exactly constrained. But read the papers!
On Thu, Oct 10, 2013 at 12:27 PM, Justin Lemkul wrote:
>
>
> On 10/10/13 12:17 PM, Martin, Erik W wrote:
>>
>>
>> Hi, I'm new to both Gromacs and OPLS. I have always used CH
On 10/10/13 12:17 PM, Martin, Erik W wrote:
Hi, I'm new to both Gromacs and OPLS. I have always used CHARMM or AMBER
before so am a bit confused about some idiosyncrasies.
When I go to a production run on my system (a protein in a truncated
octahedron box of Tip4 water) I have removed all co
Hi, I'm new to both Gromacs and OPLS. I have always used CHARMM or AMBER
before so am a bit confused about some idiosyncrasies.
When I go to a production run on my system (a protein in a truncated octahedron
box of Tip4 water) I have removed all constraints. When I run grompp, I get an
error
On 10/9/13 6:42 AM, Mass wrote:
Hi Justin
Thanks for your answer but I could not solve the problem, sorry
Can you tell me how can I fix this part? the highlighted part is your answer
I google it and found this on ubuntu forum but I followed it and still I am
getting error
up vote
0
down vote
On 10/8/13 7:28 AM, Mass wrote:
I am trying to install "DSSP" in Ubuntu 12.10, I just download it from Ubuntu
software centre but when I run it I am getting the following error, any solution? I have
checked all the mail list archive and could not solve my problem
Fatal error:
Failed to exec
I am trying to install "DSSP" in Ubuntu 12.10, I just download it from Ubuntu
software centre but when I run it I am getting the following error, any
solution? I have checked all the mail list archive and could not solve my
problem
Fatal error:
Failed to execute command: /usr/local/bin/dssp -na
On 10/3/13 11:50 AM, sa wrote:
Hi all,
I am trying to compute the order parameters for the sn1 and sn2 chains of
DOPC (CHARMM36) in bilayer . I am using the g_order tool (v4.6.3).
I have constructed for each DOPC chain two index files that contains in
the first one all the Carbon atoms where
Hi all,
I am trying to compute the order parameters for the sn1 and sn2 chains of
DOPC (CHARMM36) in bilayer . I am using the g_order tool (v4.6.3).
I have constructed for each DOPC chain two index files that contains in
the first one all the Carbon atoms where the first Carbon is C=O and the
las
Hi,
On Sep 16, 2013, at 11:23 AM, mjyang wrote:
> Dear GMX users,
>
>
> I have a question about the combination of the installation parameters. I
> compiled the fftw lib with --enable-sse2 and configured the gromacs with
> "cmake .. -DGMX_CPU_ACCELERATION=SSE4.1". I'd like to know if it
Dear GMX users,
I have a question about the combination of the installation parameters. I
compiled the fftw lib with --enable-sse2 and configured the gromacs with "cmake
.. -DGMX_CPU_ACCELERATION=SSE4.1". I'd like to know if it is ok to use such a
combination?
Many thanks.
Mingjun--
gmx
Hello,
I would like to calculate angle tetrahedral order parameter of water
molecules as defined by Chau et al (eq 3). I am using g_hydorder of
gromacs 4.6.3 with my index group containing all oxygen atoms of water:
g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out
file_2.out -n i
On 9/1/13 1:30 PM, Nidhi Katyal wrote:
I have created my files long time ago using version 4.0.7. But now
analyzing the same files using g_hbond/g_mindist using version 4.5.5
Try 4.6.3. If it still doesn't work, you can feel free to file a bug report on
redmine.gromacs.org, or otherwise ju
I have created my files long time ago using version 4.0.7. But now
analyzing the same files using g_hbond/g_mindist using version 4.5.5
On Sun, Sep 1, 2013 at 10:48 PM, Justin Lemkul wrote:
>
>
> On 9/1/13 1:17 PM, Nidhi Katyal wrote:
>
>> Even after giving same cutoff radius of 0.35nm in both,
On 9/1/13 1:17 PM, Nidhi Katyal wrote:
Even after giving same cutoff radius of 0.35nm in both, I am getting around
400 contacts per timeframe with mindist but 0 contacts with g_hbond.
What version of Gromacs are you using?
-Justin
On Sun, Sep 1, 2013 at 10:40 PM, Justin Lemkul wrote:
Even after giving same cutoff radius of 0.35nm in both, I am getting around
400 contacts per timeframe with mindist but 0 contacts with g_hbond.
On Sun, Sep 1, 2013 at 10:40 PM, Justin Lemkul wrote:
>
>
> On 9/1/13 1:08 PM, Nidhi Katyal wrote:
>
>> The two groups are: protein and cosolvent mo
On 9/1/13 1:08 PM, Nidhi Katyal wrote:
The two groups are: protein and cosolvent molecules. With g_mindist -on ,
I am getting values of around 6500 per timeframe. But then why g_hbond
giving different results.
Are you using the same cutoff radius for both?
-Justin
On Sun, Sep 1, 2013 at
The two groups are: protein and cosolvent molecules. With g_mindist -on ,
I am getting values of around 6500 per timeframe. But then why g_hbond
giving different results.
On Sun, Sep 1, 2013 at 10:23 PM, Justin Lemkul wrote:
>
>
> On 9/1/13 12:50 PM, Nidhi Katyal wrote:
>
>> Hello,
>> I would
On 9/1/13 12:50 PM, Nidhi Katyal wrote:
Hello,
I would like to calculate number of contacts between two groups, for which
I am using following command:
g_hbond -f *.xtc -s *.tpr -num *.xvg -contact -b 49000 -e 5
I am getting 0 as the output. But when I am calculating number of hydrogen
bond
Hello,
I would like to calculate number of contacts between two groups, for which
I am using following command:
g_hbond -f *.xtc -s *.tpr -num *.xvg -contact -b 49000 -e 5
I am getting 0 as the output. But when I am calculating number of hydrogen
bonds between the same two groups by using the a
Dear all
I would like to calculate angle tetrahedral order parameter of water
molecules as defined by Chau et al (eq 3). I am using g_hydorder of
gromacs 4.6.3 with my index group containing all oxygen atoms of water:
g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out
file_2.out -n
So I've added :
---
couple-moltype = Protein
couple-intramol = yes
---
and now I have non-zero dVcoul/dl, but the dVvdw/dl terms are still zero.
Why is this still zero/should I be concerned about that?
I'm also happy to no longer be seeing a 100% exchange rate (which I
previousl
Greetings,
I'm trying to use HREMD on a protein (100 residues) in water to better
sample side chain conformational space in the canonical ensemble. The free
energy part in my 8 .mdp files, with N ranging from 0 to 7, is :
---
free-energy = yes
nstdhdl = 100
init-lambda-state = N
coul-lambdas =
So open your terminal app, type
sudo apt-get install gromacs
type your password at promt
volia, gromacs is installed
2013/8/19
> I am a new user.
> I have aquestion about install gromacs.
> I want to install gromacs.
> May guide me for install gromacs?
> --
> gmx-users mailing listgmx-users
Hi!
GROMACS is in the standart Ubuntu repo, so you can simply type
sudo apt-get install gromacs
in your terminal and after successfull installation call all gromacs
utilities from the command line
If you need some special versions of GROMACS or if you want to install it
from source, you can take a
I am a new user.
I have aquestion about install gromacs.
I want to install gromacs.
May guide me for install gromacs?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/
Hi
I am a new user.
I have a questin for install gromacs on ubuntu.
May guide me for install gromacs?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before po
When I minimize a structure, I can get down to the force max being <0.01
Low-Memory BFGS Minimizer converged to Fmax < 0.01 in 6839 steps
Potential Energy = -5.12340607768673e+03
Maximum force = 6.68907856457542e-03 on atom 3029
Norm of force = 2.19978176343026e-03
kJ/nm. However, whe
On 6/17/13 4:58 PM, Hyunjin Kim wrote:
Hi,
I sent the following email last Saturday and I haven't got any reply yet.
I wonder whether you can suggest something regarding this issue.
Thanks in advance.
**
I
Hi,
I sent the following email last Saturday and I haven't got any reply yet.
I wonder whether you can suggest something regarding this issue.
Thanks in advance.
**
I edit my topology file for mutating CH --> C
Hi,
I edit my topology file for mutating CH --> COH during free energy
calculation.
Since one hydrogen atom attached to carbon disappears, while two O and H
atoms are appearing, I build topology file as follows:
8 opls_169 1TESTO 3 -0.715.9994
opls_1400.1
I appreciate you for your useful guidance
I want to determine the minimum distances between COM (center of mass)
of a surfactant molecule and that of number of other surfactants but
g_mindist compute the distances between one group and a number of
other groups. It is not quite clear for me that g_
Huyjin,
If you look in your log file from the rerun you will see that when running
using the GPU, energy groups are ignored or unused for energy reporting. Thus
for this to work you need to run it on the CPUs.
This is what I get in my output md.log when trying the same thing...
>> NOTE: With GP
>
>
> On 5/12/13 1:53 PM, Hyunjin Kim wrote:
>>>
>>>
>>> On 5/12/13 1:31 PM, Hyunjin Kim wrote:
>
>
> On 5/12/13 1:14 PM, Hyunjin Kim wrote:
>>>
>>>
>>> On 5/12/13 12:54 PM, Hyunjin Kim wrote:
>
>
> On 5/12/13 2:25 AM, Hyunjin Kim wrote:
>> De
On 5/12/13 1:53 PM, Hyunjin Kim wrote:
On 5/12/13 1:31 PM, Hyunjin Kim wrote:
On 5/12/13 1:14 PM, Hyunjin Kim wrote:
On 5/12/13 12:54 PM, Hyunjin Kim wrote:
On 5/12/13 2:25 AM, Hyunjin Kim wrote:
Dear,
I want to calculate LJ and Electrostatic energies between two
groups
defined in
>
>
> On 5/12/13 1:31 PM, Hyunjin Kim wrote:
>>>
>>>
>>> On 5/12/13 1:14 PM, Hyunjin Kim wrote:
>
>
> On 5/12/13 12:54 PM, Hyunjin Kim wrote:
>>>
>>>
>>> On 5/12/13 2:25 AM, Hyunjin Kim wrote:
Dear,
I want to calculate LJ and Electrostatic energies
On 5/12/13 1:31 PM, Hyunjin Kim wrote:
On 5/12/13 1:14 PM, Hyunjin Kim wrote:
On 5/12/13 12:54 PM, Hyunjin Kim wrote:
On 5/12/13 2:25 AM, Hyunjin Kim wrote:
Dear,
I want to calculate LJ and Electrostatic energies between two groups
defined in index.ndx during rerun with original traje
>
>
> On 5/12/13 1:14 PM, Hyunjin Kim wrote:
>>>
>>>
>>> On 5/12/13 12:54 PM, Hyunjin Kim wrote:
>
>
> On 5/12/13 2:25 AM, Hyunjin Kim wrote:
>> Dear,
>>
>> I want to calculate LJ and Electrostatic energies between two groups
>> defined in index.ndx during rerun with ori
On 5/12/13 1:14 PM, Hyunjin Kim wrote:
On 5/12/13 12:54 PM, Hyunjin Kim wrote:
On 5/12/13 2:25 AM, Hyunjin Kim wrote:
Dear,
I want to calculate LJ and Electrostatic energies between two groups
defined in index.ndx during rerun with original trajectory.
The following is what I tried:
1.
>
>
> On 5/12/13 12:54 PM, Hyunjin Kim wrote:
>>>
>>>
>>> On 5/12/13 2:25 AM, Hyunjin Kim wrote:
Dear,
I want to calculate LJ and Electrostatic energies between two groups
defined in index.ndx during rerun with original trajectory.
The following is what I tried:
>
On 5/12/13 12:54 PM, Hyunjin Kim wrote:
On 5/12/13 2:25 AM, Hyunjin Kim wrote:
Dear,
I want to calculate LJ and Electrostatic energies between two groups
defined in index.ndx during rerun with original trajectory.
The following is what I tried:
1. insert "energygrps r_1 r_25" in the test.
>
>
> On 5/12/13 2:25 AM, Hyunjin Kim wrote:
>> Dear,
>>
>> I want to calculate LJ and Electrostatic energies between two groups
>> defined in index.ndx during rerun with original trajectory.
>>
>> The following is what I tried:
>>
>> 1. insert "energygrps r_1 r_25" in the test.mdp file.
>>
>> 2. g
On 5/12/13 2:25 AM, Hyunjin Kim wrote:
Dear,
I want to calculate LJ and Electrostatic energies between two groups
defined in index.ndx during rerun with original trajectory.
The following is what I tried:
1. insert "energygrps r_1 r_25" in the test.mdp file.
2. grompp -f test.mdp -c x.gro -
Dear,
I want to calculate LJ and Electrostatic energies between two groups
defined in index.ndx during rerun with original trajectory.
The following is what I tried:
1. insert "energygrps r_1 r_25" in the test.mdp file.
2. grompp -f test.mdp -c x.gro -o x.tpr -p x.top -n index.ndx
3. mdrun -nt
On 3/7/13 8:31 AM, l@utwente.nl wrote:
Dear all,
When calculation the RDF, it asks:
Select a reference group and 1 group
Group 0 ( System) has 1600 elements
Group 1 ( Other) has 1600 elements
Group 2 ( PE) has 1600 elements
Group 3 ( a
Dear all,
When calculation the RDF, it asks:
Select a reference group and 1 group
Group 0 ( System) has 1600 elements
Group 1 ( Other) has 1600 elements
Group 2 ( PE) has 1600 elements
Group 3 ( a_1-1600) has 1600 elements
My question is wha
On Tue, Jan 29, 2013 at 4:39 PM, Susan Chacko wrote:
>
> Sorry for a newbie question -- I've built several versions of Gromacs in
> the
> past but am not very familiar with the new cmake build system.
>
> In older versions, the procedure was:
> - build the single-threaded version
>
FYI there is
On Tue, Jan 29, 2013 at 11:07 AM, Susan Chacko wrote:
> Thanks for the info! Our cluster is somewhat heterogenous, with
> some 32-core GigE-connected nodes, some older 8-core Infiniband-connected
> nodes, and some GPU nodes. So we need pretty much every variation
> of mdrun :-).
>
There is no di
Thanks for the info! Our cluster is somewhat heterogenous, with
some 32-core GigE-connected nodes, some older 8-core Infiniband-connected
nodes, and some GPU nodes. So we need pretty much every variation
of mdrun :-).
On Jan 29, 2013, at 11:00 AM, Mark Abraham wrote:
> On Tue, Jan 29, 2013 at 4:
On Tue, Jan 29, 2013 at 4:39 PM, Susan Chacko wrote:
>
> Sorry for a newbie question -- I've built several versions of Gromacs in
> the
> past but am not very familiar with the new cmake build system.
>
> In older versions, the procedure was:
> - build the single-threaded version
> - then build t
Sorry for a newbie question -- I've built several versions of Gromacs in the
past but am not very familiar with the new cmake build system.
In older versions, the procedure was:
- build the single-threaded version
- then build the MPI version of mdrun only. No need to build the other
executable
On 01/21/2013 01:31 PM, Justin Lemkul wrote:
Your cmake command needs to use -DFFTWF_INCLUDE_DIR and
-DFFTWF_LIBRARY to indicate the single-precision libraries (note that
-DFFTW_INCLUDE_DIR and -DFFTWF_INCLUDE_DIR specify different things)
or simply use -DCMAKE_PREFIX_PATH=/soft/fftw-3.3.3/ for
On 1/21/13 3:44 AM, Albert wrote:
Hello:
I am compiling the latest gromacs 4.6 with command:
cmake .. -DGMX_MPI=ON -DCMAKE_CXX_COMPILER=/soft/openmpi-1.4.3/bin/mpiCC
-DCMAKE_C_COMPILER=//soft/openmpi-1.4.3/bin/mpicc
-DCMAKE_INSTALL_PREFIX=/soft/gromacs4.6 -DGMX_GPU=OFF -DBUILD_SHARED_LIBS=O
Hello:
I am compiling the latest gromacs 4.6 with command:
cmake .. -DGMX_MPI=ON -DCMAKE_CXX_COMPILER=/soft/openmpi-1.4.3/bin/mpiCC
-DCMAKE_C_COMPILER=//soft/openmpi-1.4.3/bin/mpicc
-DCMAKE_INSTALL_PREFIX=/soft/gromacs4.6 -DGMX_GPU=OFF
-DBUILD_SHARED_LIBS=OFF -DFFTW_INCLUDE_DIR=/soft/fftw-3.
On 1/10/13 9:28 PM, Tom wrote:
Dear Gromacs Users,
I want to use dihedral constraint in gmx.
First, you should understand that constraints and restraints refer to very
different ideas:
http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
I directly type the follo
Dear Gromacs Users,
I want to use dihedral constraint in gmx.
I directly type the following onto my topol.top file :
--
[ dihedral_restraints ]
; ai ajakal type label phi dphi kfac power
; phi C'(n-1) - N - CA - C'
506505 502503
On 1/3/13 3:49 PM, hyunj...@andrew.cmu.edu wrote:
Hi,
I saw Fatemeh's and others' posts regarding gold and S FF parameters.
I have a few questions regarding this:
1. The vdW parameters for Au changed according to interaction atoms such
as C, H, N, S, etc.
However, I wonder, if the system incl
Hi,
I saw Fatemeh's and others' posts regarding gold and S FF parameters.
I have a few questions regarding this:
1. The vdW parameters for Au changed according to interaction atoms such
as C, H, N, S, etc.
However, I wonder, if the system includes both S and N, which interact
with Au, then which
On 12/27/12 8:44 PM, yeqing1211 wrote:
Hello everyone:
I prepar to make a QM/MM simulation by employing gromacs compiled
with mopac, and need to define two groups which are treated by QM and MM
separately, the question is this: during the dynamics course of my research
system, particles
Hello everyone:
I prepar to make a QM/MM simulation by employing gromacs compiled
with mopac, and need to define two groups which are treated by QM and MM
separately, the question is this: during the dynamics course of my research
system, particles will enter/leave the QM zone, so there is a
On 12/17/12 5:51 PM, Tom wrote:
Dear Gromacs Users,
I created a new residue on aminoacids.rtp file
and assigned improper dihedral after [ bonds ], for example
[ impropers ]
C2H C3 S1
Then I want to add the parameters of this dihedral angle potential
onto ffbonded.itp
I k
On Fri, Dec 14, 2012 at 3:46 PM, Thomas Schlesier wrote:
> Dear all,
> i have a small question regarding the '-nosum' option of 'mdrun'.
> The manual states:
>
> For a global thermostat and/or barostat the temperature and/or pressure
> will also only be updated every nstlist steps. With this optio
I think the same way as you. They do bring in errors but this is acceptable
in normal MD because we already have lots of approximations. BTW, -sum has
been dropped from 4.5, in other words, Gromacs won't calculate global
Energy every step by default now.
dawei
On Fri, Dec 14, 2012 at 9:46 AM, Th
Dear all,
i have a small question regarding the '-nosum' option of 'mdrun'.
The manual states:
For a global thermostat and/or barostat the temperature and/or pressure
will also only be updated every nstlist steps. With this option the
energy file will not contain averages and fluctuations over
On 12/1/12 1:54 PM, Andrew DeYoung wrote:
Hi,
I am looking at the file ffbonded.itp located in the oplsaa.ff directory
(usually located in /usr/local/gromacs/share/gromacs/top/oplsaa.ff). I see
the following entry in the [ dihedraltypes ] section:
C3 CT OH HO 3 0.418
Hi,
I am looking at the file ffbonded.itp located in the oplsaa.ff directory
(usually located in /usr/local/gromacs/share/gromacs/top/oplsaa.ff). I see
the following entry in the [ dihedraltypes ] section:
C3 CT OH HO 3 0.41840 1.25520 0.0 -1.67360
0.0 0.00
Hi,
Thank you for replies.
>> I was also facing the same problem. If you check your pressure during
>> this NPT run, u can see that it got increased to a higher value.
In my case, the situation looks slightly different.
The pressure is not increasing at all (see xvg file in [1]), though it is on
Hi, all-
I would recommend using Parrinellio-Rahman + Nose-Hoover md + at least
until 4.6.
A random-walk drift in the conserved energy is actually what MTTK
gives -- it's not as conserved as, say, energy conservation, it just
has an expectation value of zero drift over time, which means that the
Hi,
I was also facing the same problem. If you check your pressure during
this NPT run, u can see that it got increased to a higher value. I had
posted the same problem few days back, u can follow the thread. It
seems MTTK is not stable enough and is not performing well in this
context. So I have
Dear list,
I am trying to use MTTK barostat in GROMACS 4.5.5.
After analyzing the result for a while, I found that the conserved energy (not
total energy) of MTTK is drifting during the simulation.
The .xvg, .edr files are uploaded at [1] and [2]. It is drifting with a
constant ratio of ca. -185
Hi Thomas,
On Nov 12, 2012, at 5:18 PM, Thomas Schlesier 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: 4.0.7 and 4.5.
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 fma4
Hi,
If you have time, I have a question about the OPLS parameters given in the
files located in the "top" directory (for example,
/usr/local/gromacs/share/gromacs/top/oplsaa.ff).
In the oplsaa.ff directory, there is a file atomtypes.atp. At the top of
this file, it says:
; Types 1-134 are fro
On 10/23/12 2:18 AM, Davoud Zare wrote:
Dear Sir
I am a newbie on Gromacs. I am trying to solvate my protein (1CJ5.pdb) with
water. I am following the tutorial by Justin Lemkul but when I execute the
following command
pdb2gmx -f 1CJ5.pdb -o 1CJ5_processed.gro -water spce
and choose OPLS-AA/L
Dear Sir
I am a newbie on Gromacs. I am trying to solvate my protein (1CJ5.pdb) with
water. I am following the tutorial by Justin Lemkul but when I execute the
following command
pdb2gmx -f 1CJ5.pdb -o 1CJ5_processed.gro -water spce
and choose OPLS-AA/L all-atom force field
I am getting an fatal
...@rostlab.informatik.tu-muenchen.de
> Gesendet: Donnerstag, 18. Oktober 2012 15:28
> An: Discussion list for GROMACS users
> Betreff: Re: AW: [gmx-users] question about the minimization
>
> Hi Justin,
> I am sorry, I switched the radius and the numbers:
> radius=0
> charge=1
> ma
Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im
Auftrag von reising...@rostlab.informatik.tu-muenchen.de
Gesendet: Donnerstag, 18. Oktober 2012 15:28
An: Discussion list for GROMACS users
Betreff: Re: AW: [gmx-users] question about the minimization
Hi Justin
t;>>>>
>>>>>>>> Step 1114, time 2.228 (ps) LINCS WARNING
>>>>>>>> relative constraint deviation after LINCS:
>>>>>>>> rms 0.000169, max 0.001796 (between atoms 3480 and 3482)
>>>>>>>> bo
. Oktober 2012 10:56
An: gmx-users@gromacs.org
Betreff: [gmx-users] question about the minimization
Hi everybody,
I have a question about the minimization of my protein. For this
minimization I fixed the backbone and the membrane atoms which
around
my
protein.
I minimized it 3 steps long but a
>>>>> atom 1 atom 2 angle previous, current, constraint length
>>>>>> 2002 2005 30.40.1090 0.1090 0.1090
>>>>>>
>>>>>>
>>>>>>
>>>>>> And in the end there is the error:
&g
t;>>> What do you think?
>>>>
>>>> Thanks again!!
>>>>
>>>>
>>>>> Hi Eva,
>>>>>
>>>>> The change in energy in every step became smaller than the machine
>>>>> precision can represent (as is st
o:gmx-users-boun...@gromacs.org]
Im Auftrag von reising...@rostlab.informatik.tu-muenchen.de
Gesendet: Donnerstag, 18. Oktober 2012 10:56
An: gmx-users@gromacs.org
Betreff: [gmx-users] question about the minimization
Hi everybody,
I have a question about the minimization of my protein. For this
minimization I fi
;> Hi Eva,
>>>>
>>>> The change in energy in every step became smaller than the machine
>>>> precision can represent (as is stated in the output). In other words:
>>>> your
>>>> system is minimized to a very high degree.
>>>> A
ain!!
>>>>
>>>>
>>>>> Hi Eva,
>>>>>
>>>>> The change in energy in every step became smaller than the machine
>>>>> precision can represent (as is stated in the output). In other words:
>>>>> your
>&g
ation seems pretty high to me.
Cheers,
Felix
-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org]
Im Auftrag von reising...@rostlab.informatik.tu-muenchen.de
Gesendet: Donnerstag, 18. Oktober 2012 10:56
An: gmx-users@gromacs.org
Betreff: [gmx-users] ques
gh degree.
>>> A value of 10 for the Fmax is very low for a system like yours, even
>>> with
>>> a pure protein in water system you probably wouldn't hit this value.
>>> Furthermore, 30.000 steps for a minimization seems pretty high to me.
>>>
>>
gt;> Cheers,
>> Felix
>>
>> -Ursprüngliche Nachricht-
>> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
>> Im Auftrag von reising...@rostlab.informatik.tu-muenchen.de
>> Gesendet: Donnerstag, 18. Oktober 2012 10:56
>>
s-boun...@gromacs.org]
> Im Auftrag von reising...@rostlab.informatik.tu-muenchen.de
> Gesendet: Donnerstag, 18. Oktober 2012 10:56
> An: gmx-users@gromacs.org
> Betreff: [gmx-users] question about the minimization
>
> Hi everybody,
>
> I have a question about the minimization of my protein. Fo
On Thu, Oct 18, 2012 at 10:53 AM,
wrote:
> Steepest Descents converged to machine precision in 20385 steps,
> but did not reach the requested Fmax < 10.
> Potential Energy = -8.8805600e+05
> Maximum force = 3.2341940e+02 on atom 3050
> Norm of force = 2.0930219e+00
>
> I do not see why
en.de
Gesendet: Donnerstag, 18. Oktober 2012 10:56
An: gmx-users@gromacs.org
Betreff: [gmx-users] question about the minimization
Hi everybody,
I have a question about the minimization of my protein. For this minimization I
fixed the backbone and the membrane atoms which around my protein.
I mini
Hi everybody,
I have a question about the minimization of my protein. For this
minimization I fixed the backbone and the membrane atoms which around my
protein.
I minimized it 3 steps long but after step 20385 it stops with the
output:
Steepest Descents converged to machine precision in 2038
On 10/12/12 9:39 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to do a md run for my membrane protein. For this I first did the
energy minimization run.
This finished with no errors. Here is the output of it:
Steepest Descents did not converge to Fmax < 10 in 500
Hi everybody,
I want to do a md run for my membrane protein. For this I first did the
energy minimization run.
This finished with no errors. Here is the output of it:
Steepest Descents did not converge to Fmax < 10 in 5001 steps.
Potential Energy = -8.7463000e+05
Maximum force = 4.5984982e+0
Hi Justin,
thank you very much for the helpful and fast answer :)
>
>
> On 10/1/12 4:59 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi everybody,
>> I want to do a md run. But I have a problem. I have additional
>> residues
>> which are not in the aminoacid.rtp file.
>> I already
On 10/1/12 4:59 PM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to do a md run. But I have a problem. I have additional residues
which are not in the aminoacid.rtp file.
I already read the site about "Adding a Residue to a Force Field".
But the problem is that I a
Hi everybody,
I want to do a md run. But I have a problem. I have additional residues
which are not in the aminoacid.rtp file.
I already read the site about "Adding a Residue to a Force Field".
But the problem is that I am not allowed to change anything at the
topology files on the server I want t
On 9/4/12 7:51 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Ah okey, thank you.
But now I have another question. Where can I get the charge and the
chargegroup of the atoms of my residue?
I have a serine with a phosphate on it. But I do not know the charges of
the atoms. Can you give
Ah okey, thank you.
But now I have another question. Where can I get the charge and the
chargegroup of the atoms of my residue?
I have a serine with a phosphate on it. But I do not know the charges of
the atoms. Can you give me a hint where I can find them?
Thank you
>
>
> On 9/4/12 7:37 AM, reisin
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