On Fri, Mar 2, 2012 at 3:55 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 2/03/2012 6:52 PM, lina wrote:
Hi,
is the old dssp not compatible with the gromacs 4.5.5 ?
I am confused,
Thanks,
Best regards,
The new DSSP is not compatible with any GROMACS
Ha ... the dssp complain the
Gromacs' 4.5.5 do_dssp is broken. There is a patch for it in git. I haven't
tried it out, so I can't say for sure it works. This is not a DSSP problem,
it's a Gromacs problem. Just to reinforce the idea, the new DSSP should not
be used, no matter which Gromacs version you're using.
Best regards,
Dear Rama,
Since the latest version, I have to use -noappend and then just concantenate
them when they are finished. I gave up as no mater how many paths to files,
listening to the error messages, I supplied to the mdrun it still complained.
Dont know if this is a personalized bug or more
Hi,
First I thought that there might be a memory leak which could have
caused this if you ran for really long time. However, I've just ran
the very same benchmark (dhfr with PME) for one hour, monitored the
memory usage and I couldn't see any change whatsoever (see the plot
attached).
I've
Lara Bunte wrote:
Hello
I got this error:
Fatal error:
Atom ON1 is used in an interaction of type improper in the topology
database, but an atom of that name was not found in residue
number 1.
What do this mean? How to fix it?
The Atom ON1 is declared in atomtypes.atp file.
In my
Hi
In a supporting Information of a paper is written:
The description of the LF radical force fields is complete, as soon as also
the parameters of the Lennard-Jones potentials are given. For these parameters
we adopt the values specified in the CHARMM22 force field for the basic atom
types
Hi, Mark,
Thank you for help. It works. But now I have new fatal error:
Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (2)
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all
bo.shuang wrote:
Hi, Mark,
Thank you for help. It works. But now I have new fatal error:
Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (2)
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.
NOTE: invoking MPI_ABORT causes
On 2012-03-02 05:25:01PM +, Steven Neumann wrote:
Dear Gmx Users,
I run nvt simulation with small timestep with implicit solvent for 500 ps.
I used particle decomposition for this run (-pd). No I want to extend my
simulation with different mdp file from the previous nvt using:
Hi
The first part in a .rtp file is the [ bondedtypes ] with syntax
[ bondedtypes ]
; bonds angles dihedrals impropers
1 1 1 2
1.)
What do this numbers mean? I found nothing in the manual to that.
2.)
If you have improper dihedrals,
Please help :-(
Greetings
Lara
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Lara Bunte wrote:
Please help :-(
Please realize that you're asking for free help from a global mailing list. You
may not get a reply from someone immediately, as that person may be busy with
their own work, or even asleep ;)
From your original post:
In a supporting Information of a
Lara Bunte wrote:
Hi
The first part in a .rtp file is the [ bondedtypes ] with syntax
[ bondedtypes ]
; bondsanglesdihedralsimpropers
1 1 1 2
1.)
What do this numbers mean? I found nothing in the manual to that.
They are the
Thank you for help! Is that possible to run REMD on a PC with only one
processor?
Bo
bo.shuang wrote:
Hi, Mark,
Thank you for help. It works. But now I have new fatal error:
Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (2)
MPI_ABORT was invoked on
On 3/03/2012 5:17 AM, Lara Bunte wrote:
Hi
The first part in a .rtp file is the [ bondedtypes ] with syntax
[ bondedtypes ]
; bondsanglesdihedralsimpropers
1 1 1 2
1.)
What do this numbers mean? I found nothing in the manual to
On 3/03/2012 7:34 AM, bo.shuang wrote:
Thank you for help! Is that possible to run REMD on a PC with only one
processor?
No. See http://www.gromacs.org/Documentation/How-tos/REMD
Mark
Bo
bo.shuang wrote:
Hi, Mark,
Thank you for help. It works. But now I have new fatal error:
Fatal
Dear gmx users,
It seems that I have found a strange temperature value after NVT equilibrium
for 200 ps. I simulate a CNT with two graphite sheets in water box. I do not
want to them to deform or change their shaps, So I use a very large position
restraint (1*10^6) to keep their shaps. The
Dear all,
Iam trying to generate secondary structure plot through do_dssp program,
but there was an error like segmentation fault
Reading file md.tpr, VERSION 4.0.7 (single precision)
Reading file md.tpr, VERSION 4.0.7 (single precision)
Segmentation fault (core dumped)
bash-4.1#
can anybody
On 3/03/2012 5:14 PM, arun kumar wrote:
Dear all,
Iam trying to generate secondary structure plot through do_dssp
program, but there was an error like segmentation fault
Reading file md.tpr, VERSION 4.0.7 (single precision)
Reading file md.tpr, VERSION 4.0.7 (single precision)
Segmentation
On 3/03/2012 5:08 PM, zhongjin wrote:
Dear gmx users,
It seems that I have found a strange temperature value after NVT
equilibrium for 200 ps. I simulate a CNT with two graphite sheets in
water box. I do not want to them to deform or change their shaps, So I
use a very large position
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