Hi,
Pymol is sort of semi commercial. You can install it easily on Ubuntu,
using apt-get install pymol (free!), you can install from source (also
free!). You can obtain an educational build (also free!, though
requiring registration). Any will do for the building of sequences,
which on linux is as
Hello,
I am trying to run the dhfr-impl-1nm.bench benchmark but this keeps failing. I
am using Gromacs 4.5.3 built using both Intel and PGI compilers, but both
builds fail with the error message:
MPI Application rank 1 exited before MPI_Finalize() with status 0
The rank and the status value va
On 4/20/2011 6:57 PM, Miah Wadud Dr (ITCS) wrote:
Hello,
I am trying to run the dhfr-impl-1nm.bench benchmark but this keeps failing. I
am using Gromacs 4.5.3 built using both Intel and PGI compilers, but both
builds fail with the error message:
MPI Application rank 1 exited before MPI_Finali
I had the issue of shared libraries while installing which I did
troubleshoot and the installation went without any errors. I tried
converting the pdb file to a new one using editconf and it runs perfectly
fine. So, there is some issue with pdb2gmx, which I am not able to detect.
Any hints will be
Ragothaman Yennamalli wrote:
I had the issue of shared libraries while installing which I did
troubleshoot and the installation went without any errors. I tried
converting the pdb file to a new one using editconf and it runs
perfectly fine. So, there is some issue with pdb2gmx, which I am not
These were the exact commands used to install fftw 3.2.2
./configure --prefix=/export/home/raghu/fftw --enable-float --enable-shared
CC=cc F77=f77
make -j 48
make install
These were the exact commands used to install gromacs4.5.4
./configure --prefix=/export/home/raghu/gromacs --with-fft=fftw3
-
Hi everyone
I am trying to run a simulation of Alpo (aluminophosphates) microporous
material, the topology of the material was build using x2top (it had been
checked). I got all the bonding and nonbonding parameters, when I run the
energy minimization of this system, Iget this :
Steepest Desce
The MPI library is able to run other MPI jobs as well as other parallel Gromacs
runs, and it just seems like this run causes this difficulty. I am using
Platform MPI 8.1.
Regards,
Wadud.
>-Original Message-
>From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
>
Ragothaman Yennamalli wrote:
These were the exact commands used to install fftw 3.2.2
./configure --prefix=/export/home/raghu/fftw --enable-float
--enable-shared CC=cc F77=f77
make -j 48
make install
These were the exact commands used to install gromacs4.5.4
./configure --prefix=/export/ho
Hernan Ahumada wrote:
Hi everyone
I am trying to run a simulation of Alpo (aluminophosphates) microporous
material, the topology of the material was build using x2top (it had been
checked). I got all the bonding and nonbonding parameters, when I run the
energy minimization of this system, I
Dear Justin,
Thanks for the mail. Yes, without these CFLAGS the "make" was not
successful. Yes I did set the CPPFLAGS and LDFLAGS before configuring
gromacs. Since without it it would have stopped compiling. I want to agree
with you that it is some issue with shared libraries, but i dont think it
There is another free tool (Avogadro) which is pretty easy to handle this
also.
Try
http://avogadro.openmolecules.net/wiki/Get_Avogadro
in Build --> Inert ---> Peptides,
Which is very easy to use. you can choose Straight line, beta sheet or alpha
helix or other.
and save as .pdb
lina
--
gmx-
apt-get install avogadro
http://avogadro.openmolecules.net/wiki/Distribution_Packages
On Wed, Apr 20, 2011 at 10:34 PM, ZHAO Lina wrote:
> There is another free tool (Avogadro) which is pretty easy to handle this
> also.
>
> Try
>
> http://avogadro.openmolecules.net/wiki/Get_Avogadro
>
> in Bu
Ragothaman Yennamalli wrote:
Dear Justin,
Thanks for the mail. Yes, without these CFLAGS the "make" was not
successful. Yes I did set the CPPFLAGS and LDFLAGS before configuring
gromacs. Since without it it would have stopped compiling. I want to
agree with you that it is some issue with sh
On Wed, Apr 20, 2011 at 9:46 AM, Justin A. Lemkul wrote:
>
>
> Ragothaman Yennamalli wrote:
>
>> Dear Justin,
>>
>> Thanks for the mail. Yes, without these CFLAGS the "make" was not
>> successful. Yes I did set the CPPFLAGS and LDFLAGS before configuring
>> gromacs. Since without it it would have
I've never seen the -D_POSIX_PTHREAD_SEMANTICS before. What caused
you to need to define that flag?
Also...what hardware (cpu) and operating system (linux? what distro?
what version?) are you using?
Matt Z.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/list
I'm a recent gromacs user and right now I'm starting to calculate velocity
autocorrelation functions for a pure compound, using g_velacc.
I'd like to know something more about the properties and consequences of the
option -mol and what exactly the program does if the option is not included.
I'm
On 2011-04-20 18.30, Luis Martins wrote:
I'm a recent gromacs user and right now I'm starting to calculate
velocity autocorrelation functions for a pure compound, using g_velacc.
I'd like to know something more about the properties and consequences of
the option -mol and what exactly the program
Hello,
I am trying to obtain the density for my system that is exactly identical to
experimental value but whatever pressure I apply density is still off by 3%.
Is this issue common?
--
Thanks,
Jennifer N.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listi
On 2011-04-20 19.40, Juliette N. wrote:
Hello,
I am trying to obtain the density for my system that is exactly
identical to experimental value but whatever pressure I apply density is
still off by 3%.
Is this issue common?
--
Thanks,
Jennifer N.
Yes, force fields are not perfect.
How about run
Hi David,
I used to apply NPT to fix the density, how can I get the denisty using NVT?
On 20 April 2011 13:46, David van der Spoel wrote:
> On 2011-04-20 19.40, Juliette N. wrote:
>
>> Hello,
>>
>> I am trying to obtain the density for my system that is exactly
>> identical to experimental valu
On 2011-04-20 20.10, Juliette N. wrote:
Hi David,
I used to apply NPT to fix the density, how can I get the denisty using NVT?
You turn off P coupling and fix the right density by scaling using editconf.
On 20 April 2011 13:46, David van der Spoel mailto:sp...@xray.bmc.uu.se>> wrote:
On
Dear All,
I tried to minimize the energy of CNT-DNA system in vacuum (just to make sure
it
works) using l-bfgs integrator. When I run in the .trr output file, ends of dna
only move slightly towards cnt, but it doesn't wrap around it. Could anyone
please guide me what can be the possible issues
majid hasan wrote:
Dear All,
I tried to minimize the energy of CNT-DNA system in vacuum (just to make
sure it works) using l-bfgs integrator. When I run in the .trr output
file, ends of dna only move slightly towards cnt, but it doesn't wrap
around it. Could anyone please guide me what can
It is a SunOS operating system, 64 bit with Eight 6-core AMD opteron CPUs.
On Wed, Apr 20, 2011 at 11:34 AM, Matthew Zwier wrote:
> I've never seen the -D_POSIX_PTHREAD_SEMANTICS before. What caused
> you to need to define that flag?
>
> Also...what hardware (cpu) and operating system (linux? w
Thanks. I'm no Sun expert, so I'd have to echo Justin's request for
the precise sequence of commands you used to install GROMACS and all
dependencies.
On Wed, Apr 20, 2011 at 2:51 PM, Ragothaman Yennamalli
wrote:
> It is a SunOS operating system, 64 bit with Eight 6-core AMD opteron CPUs.
>
> On
Okay, thanks. But then does it make any big difference on mdrun if we don't
minimize energy first?
And one more thing, any idea how long it may take to run md for 367 atoms on a
laptop with 2GB ram, and dual core 1.4GHz processor. I am just wondering if it
is possible to get any results from md
majid hasan wrote:
Okay, thanks. But then does it make any big difference on mdrun if we
don't minimize energy first?
You should always run energy minimization. What I'm saying is that you should
not expect to see any major changes or important phenomena evolve when simply
running EM.
Matthew Zwier wrote:
Thanks. I'm no Sun expert, so I'd have to echo Justin's request for
the precise sequence of commands you used to install GROMACS and all
dependencies.
In addition, you can add -g to your CFLAGS to get debugging symbols, then
execute pdb2gmx via a debugger like gdb. Th
Hello gmx-users
I have 2 dynamic, one is the continuation of the other. The problem is that
both start at time 0.Is there any way to change the dynamic time in order to
concatenate
both?
Thanks in advance.
Víctor E. Bahamonde Padilla
Laboratorio de Fisicoquímica Molecular
Departamento de Química
Okay, thanks a lot.
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Wed, April 20, 2011 12:01:33 PM
Subject: Re: [gmx-users] L-BFGS energy minimization not leading to wrapping of
dna around cnt
majid hasan wrote:
> Okay, thanks. But then does it
Víctor Bahamonde wrote:
Hello gmx-users
I have 2 dynamic, one is the continuation of the other. The problem is
that both start at time 0.
Is there any way to change the dynamic time in order to concatenate
both?
trjcat -settime.
-Justin
Thanks in advance.
/Víctor E. Bahamonde Padilla
L
I have a fairly stupid question about restart from a checkpoint and binary
identical messages, probably because I can't understand the doco.
When I restart (or extend) a double-precision run from a checkpoint involving
either dlb or even a different decomposition count (say I changed the number o
On 4/21/2011 8:00 AM, Peter C. Lai wrote:
I have a fairly stupid question about restart from a checkpoint and binary
identical messages, probably because I can't understand the doco.
When I restart (or extend) a double-precision run from a checkpoint involving
either dlb or even a different deco
Also why the make -j 48, when you only have 8 cores?
I'm not even sure if the linker is ok with make -jN for building gromacs, it
is not listed as compatible for *BSD ports. Also, does your make (I imagine
this is Solaris make) have all the same semantics as gnu-make (gmake)?
And why did you swi
On 4/20/2011 11:17 PM, Miah Wadud Dr (ITCS) wrote:
The MPI library is able to run other MPI jobs as well as other parallel Gromacs
runs, and it just seems like this run causes this difficulty. I am using
Platform MPI 8.1.
OK. That covers just one of the points I raised...
Mark
-Origina
Hi,
I was trying to calculate the dipole moment of part of my peptide. In other
words, if I have a 10-residue peptide, I was interested in calculating the
dipole-moment contribution of the backbone. So, I made an index file which have
a group containing backbone atoms. But, if I try to use g_d
Hi gromacs users,
I am working on Photo active yellow protein.
Although i successfully build the force field and patched the
chromophore to the protein.
After energy minimizing the protein, the chromophore flies away separately.
I don't know whether i am missing anything?
Please help.
Ram
Isn't the chromophore supposed to be covalently bonded to the protein?
My cursory search shows Vengris et al 2004 in Biophys. J. citing Baca et al
1994 and van Beeumen et al 1993: "This small 125-residue protein contains a
p-coumaric acid chromophore that is covalently bound to the protein backbone
Yes, you are right, the chromophore(p-coumaric acid) is covalently bonded to
the Sulphur(S) atom of the Cys-69 residue.
But I specified the covalent bond in my topology.
[ bonds]
C +SG
[ angles ]
OC +SG
CA1 C +SG
C +SG +CB
[ dihedrals ]
O C +SG+CB
Hi,
I was trying to calculate the dipole moment of part of my peptide. In other
words, if I have a 10-residue peptide, I was interested in calculating the
dipole-moment contribution of the backbone. So, I made an index file which have
a group containing backbone atoms. But, if I try to use g_d
On 4/21/2011 10:12 AM, Ramachandran G wrote:
Yes, you are right, the chromophore(p-coumaric acid) is covalently
bonded to the Sulphur(S) atom of the Cys-69 residue.
But I specified the covalent bond in my topology.
[ bonds]
C +SG
That's your .rtp entry. What's in your [molecules] section
On 4/21/2011 10:17 AM, Sanku M wrote:
Hi,
I was trying to calculate the dipole moment of part of my peptide.
In other words, if I have a 10-residue peptide, I was interested in
calculating the dipole-moment contribution of the backbone. So, I made
an index file which have a group containing
On 4/21/2011 10:33 AM, Mark Abraham wrote:
On 4/21/2011 10:17 AM, Sanku M wrote:
Hi,
I was trying to calculate the dipole moment of part of my peptide.
In other words, if I have a 10-residue peptide, I was interested in
calculating the dipole-moment contribution of the backbone. So, I
made
Dear All,
I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then
ran
the mdrun with integrator = md. I am using a small ssDNA consisting of two
residues only (66 atoms), and a small CNT of about 80 atoms.
My commands are:
For energy minimization,
grompp -f lbfgs.mdp -po
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