On Sun, Jun 26, 2011 at 14:09, wrote:
> /bin/sh: line 0: cd: include: No such file or directory
There's a mistake in the Makefile: include is one level higher, but is
treated as if it would be in the current level and a "cd .." is done
afterwards. You can move include into src, or just add a lin
On Fri, Apr 20, 2012 at 14:49, Olivia Waring wrote:
> My invocation of mdrun, using 8 processors and the following mdp file:
> ...
> There are: 1184 Atoms
> ...
> DD step 4 load imb.: force 181.0%
>
> Not all bonded interactions have been properly assigned to the domain
> decomposition cells
Hi
On Wed, Jan 2, 2013 at 1:15 PM, James Starlight wrote:
> so why my simulation of the sp3 lattice have been crashed with the
> links warnings ( which always tells about wrong geometry in topology)?
I might have missed something from the beginning of this discussion...
Why do you use LINCS with a l
On Wed, Jan 2, 2013 at 2:58 PM, James Starlight wrote:
> By the way now I'd like to simulate the same 2D flexible ( in non
> planar hybridization) lattice but consist of non-hydrogens atoms only
> ( only atoms forming lattice scaffold ). Does it possible to change
> Carbon atom-valence (from 4 to
On Sun, Jan 6, 2013 at 1:44 PM, James Starlight wrote:
> I mean absence of exponential factor in the C6 term :)
>
> So to change the vdw radius of the specified atom I should to varry
> both c6 and c12 shouldn't it ?
Hmm, to me these look like very basic force field questions. Did you
try to look
On Sat, Jan 12, 2013 at 10:04 AM, ramesh cheerla
wrote:
> This probably means your
> constraint lengths are too long compared to the domain decomposition cell
> size. Decrease the number of domain decomposition grid cells
This gives another possible solution. You decrease the number of DD
grid ce
On Mon, Jan 14, 2013 at 9:23 PM, santhosh wrote:
> I want to output pdb during the run. Before every integration step, I want
> to output the current configuration of the system.
Before an integration step is after the previous integration step,
which is where the normal trajectory writing happen
On Thu, Jan 17, 2013 at 10:59 AM, James Starlight
wrote:
> thank you for so detailed explanation.
You're welcome. Now it's up to you to use it :)
> Now it's only intresting to me
> if it possible to change vdw radius (assuming it as the distance from
> center of atom to it outer electronic shell
On Thu, Jan 17, 2013 at 1:51 PM, James Starlight wrote:
> So if I have force field with the C6/C12 terms (instead of
> sigma\epsilon) I need to express sigma (which correspond to the Rmin
> in LJ equation) as the (C12/C6)^0.5. Than if I want to increase sigma
> ( and consequently to increase vdw
On Mon, Jan 21, 2013 at 7:06 PM, Marcin, Zachary
wrote
> dvxx+= x[i][xx] *f[i][XX];
>
Compare the indexing above with:
> This is the same as the formula that I am trying to solve for (Vi*Pi +
> .5*SUM(Rij * Fij)).
>
... the ones you want to have. See the difference ? The existing code takes
on
On Thu, Feb 7, 2013 at 8:13 PM, Yun Shi wrote:
> So instead of making an index file with 399 groups of each residue in
> A and typing in rerun.mdp file 400 group names as
> "energygrps = A1 A2 A3 A4 ... A399 B", and issuing g_energy command 399 times,
There can be maximum 256 groups defined at on
On Mon, Feb 18, 2013 at 12:10 PM, Mark Abraham wrote:
> b) a particle needs to be at that immobile reference point - you can
> measure a distance to a point whether or not there is something there.
I'm not sure that it's the same use-case... I recently talked to
someone trying to define such a fi
On Tue, Feb 19, 2013 at 1:32 PM, Tomek Wlodarski
wrote:
> The problem is that this is only message I got...
But that's an important error. GROMACS 4.6 depends a lot on the
compiler generated code, as opposed to 4.5 and previous which used
hand-written assembler code. The build procedure detects t
On Fri, Aug 31, 2012 at 1:45 PM, Steinbrecher, Thomas (IPC)
wrote:
> However, when I make the following two changes in my input file:
>
> pull_start = no
> pull_init1 = 1.95
>
> which should (?) amount to an equivalent setup, a very different trajectory
> results in which the COM distan
On Fri, Aug 31, 2012 at 8:42 PM, mohan maruthi sena
wrote:
> Hi all,
> I have built topology for elastic network as follows(the
> atoms which fall with in a distance less than 6 angtroms are bonded).
> [bonds]
> ;aiaj funct bo kb
> 2 1 1 3.80
On Wed, Sep 5, 2012 at 8:37 PM, Peter C. Lai wrote:
> Could be a result of not setting x/y compressibility = 0 as the manual
> suggests you should do...
As one who has also tried to use walls recently, I've also found this
statement in the manual, but no further explanation. Anyone cares to
expan
On Sat, Oct 6, 2012 at 6:03 PM, Dr. Vitaly Chaban wrote:
> Would anyone perhaps suggest some tricks to increase the stability of
> the highly parallel jobs (NP > 100), which use domain decomposition
> among nodes.
It would be more helpful to know what you are talking about, i.e. a
definition of s
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
On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall wrote:
> Thanks Justin. I identified the offending waters using vmd (adding 1 to
> resID and atom number since vmd starts counting at 0) and checked
> confout.gro to make sure the coordinates matched up. I only have one group
> for all frozen atoms in
Hi Andrew!
In addition to Justin's reply, I would like to point out that this is
something you can easily answer yourself by building a few atoms
system using your .itp file and running gmxdump to look at the actual
values stored in the .tpr.
Cheers,
Bogdan
On Sat, Dec 8, 2012 at 6:53 PM, Andrew
Hi Andrew!
I've also been a bit confused by the names when I started looking at
the force field definitions in GROMACS. Although Justin's replies
contain all the information (as usual :)), let's try to shed some
light with an example: consider a chain formed by atoms i-j-k-l-m-n; -
means that ther
On Fri, Aug 12, 2011 at 19:23, Justin A. Lemkul wrote:
> Try setting the environment variable GMX_MAXBACKUP to zero.
This environment variable is read only by the 4.5 series. In 4.0.7
there is no way to control it, there is a hard-coded limit of 128.
Cheers,
Bogdan
--
gmx-users mailing list
On Sat, Aug 13, 2011 at 05:43, Amit Choubey wrote:
> The largest charge group contains 267 atoms. The maximum is 32.
Column 6 in the [atoms] section of the .top file defines the charge
group. If you want each atom to be in its own charge group, you can
set this to the same number as the atom numb
On Fri, Aug 19, 2011 at 20:02, Dr. Vitaly V. Chaban wrote:
> What criterion does the grompp utility use to identify H-atoms when it
> is requested in the MDP file to apply constraints=h-bonds? Thanks.
Any atom name starting with H or h (so case-insensitive).
Cheers,
Bogdan
--
gmx-users mailing
On Wed, Dec 21, 2011 at 18:44, SebastianWaltz
wrote:
> Hi all,
>
> I try to reproduce the results from g_angle using my own c++ code. Using
> the formula
>
> θ=acos(r_ij * r_kj/|r_ij||r_kj|)
>
> with the acos from the cmath library, I obtain an angle which is always
> ~5% larger when the angel cal
Hi Prentice,
The subject and first phrase mention version 4.6.3, but all scripts
refer to 4.6.2. Are you sure you are not mixing versions ? Do you have
another 4.6.x version working already ?
> -DCMAKE_C_FLAGS="-O3 -qarch=450d -qtune=450" \
Could you try with a lower optimization level ?
> B
On Wed, Aug 7, 2013 at 5:04 PM, Prentice Bisbal
wrote:
> I couldn't find anything explicit in the documentation, The compute node
> kernel (CNK) is proprietary, but is said to be very Linux-like, so a signal
> 6 should be the same as on Linux, which would be an abort signal.
There are several cal
2010/10/22 C. Batistakis
>
> Dear Justin
>
> Actually, what I want to do is to kill the attraction part of the LJ
> substrate-polymer interaction. So, I was thinking to put the cut-off equal
> the 1,12σ (point with the lowest energy).
>
> Do you have any other idea how can I have only the repuls
On Thu, Nov 4, 2010 at 1:08 AM, Roland Schulz wrote:
> BTW: Is it somehow possible to print the kernel error messages that are
> shown by dmesg to the user from within GROMACS? That would help the user to
> directly see the reason of the error. Thus I'm looking for a function
> similar to strerror
On Fri, Nov 19, 2010 at 12:15, Reiner Ribarics
wrote:
> Our group has already done some rather long simulations and according to the
> script files forces are written every 1 steps and can be accessed via
> trjconv with -cf option that assigns each atom a temperature factor. I was
> wondering
On Mon, Nov 29, 2010 at 16:16, sreelakshmi ramesh
wrote:
> so can anybody tell me how to hack the trr file so that i can change the
> velocity parameter in it
You can use the xdrfile library to read in a certain frame of the trr
file, change the velocity in the array that you get, then use the
xd
On Tue, Jan 11, 2011 at 14:19, Justin A. Lemkul wrote:
>
>
> Sergio Manzetti wrote:
>>
>> Hi Justin, it was a blank ./configure
This defaults to something else than /usr/lib...
> I don't know why a standard location like /usr/lib isn't be detected as
> containing the libraries, but you can set L
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