Can anyone from development comment on this? I see that now 4.6 is coming
out ... if this is a bug in the code, it would be nice if it's fixed in 4.6.
Greg
On Thu, Apr 26, 2012 at 11:00 AM, Yongchul Chung wrote:
> Hi all,
>
> I am carrying out energy minimization on bulk pol
I suppose I can calculate virial manually ... but thought there might be a
glitch in the code when making a transition from 4.0 to 4.5. I sent an
e-mail to gmx-developers.
Greg
On Thu, Apr 26, 2012 at 1:00 PM, Justin A. Lemkul wrote:
>
>
> On 4/26/12 12:36 PM, Yongchul Chung wrote:
Hi all,
I am carrying out energy minimization on bulk polymer system (N~2) with
integrator = l-bfgs in double precision gromacs 4.5.5. I am using
tabulated force-fields for bonded, and non-bonded interactions. In the
force field, the coulombic interaction is set to zero, hence, the output is
Hi all,
I've carried out the normal mode analysis on my system using g_nmeig
command, and from this, I have eigenfreq.xvg, eigenval.xvg, and
eigenvec.trr.
However, I was not aware that I can set the number of eigenvector/frequency
to be written on XVG files (default is 1 to 50 lowest), and now wa
Please disregard this post ... I found it in autocorr.c
On Wed, Mar 7, 2012 at 2:09 PM, Yongchul Chung wrote:
> Hi,
>
> I am trying to locate code for angle auto-correlation function (ACF)
> in GROMACS 4.0.7. Angle ACF is calculated by g_rotacf for GROMACS
> (gmx_rotacf.c).
Hi,
I am trying to locate code for angle auto-correlation function (ACF)
in GROMACS 4.0.7. Angle ACF is calculated by g_rotacf for GROMACS
(gmx_rotacf.c). In line 194 of gmx_rotacf.c, it calls "do_autocorr".
This function is in gstat.h file line 125 - 185. But I don't see any
actual code which ca
does not start before the ones in the background finished by
> using the command 'wait':
>
> mdrun -deffnm [...] &
> wait
> grompp [...]
> mdrun -deffnm [...] &
> wait
> echo FINISHED
>
> Hope it helps,
>
> Tsjerk
>
> On Thu, Aug 25, 201
Hello gmx-users,
I am trying to run a sequence of energy minimizations for a model polymer
system. Currently, I do following steps manually:
step 1) I run an energy minimization for a configuration. (using mdrun
option)
step 2) From the output of this configuration, I change something in the
coord
On Sat, Nov 20, 2010 at 12:54 AM, Sunita Patel
wrote:
> Dear Users,
>
> I calculated RMSD for a trajectory with same reference structure using
> GROMACS
> and VMD. I observed completely difference plots for the same data. Please
> see
> the attached file.
>
> What could be the cause for this dispa
Thanks, Mark.
Greg
On Sat, Nov 13, 2010 at 12:35 PM, Mark Abraham wrote:
> On 14/11/2010 4:06 AM, Yongchul Chung wrote:
>
> Thanks Justin for your prompt reply. I am aware of the link you provided,
> but it seems they are rather hand-waving. It would be nice if I could be
>
Forgot to mention that I am using gromacs 4.0.3 with N=19200
Greg
On Sat, Nov 13, 2010 at 12:06 PM, Yongchul Chung wrote:
> Thanks Justin for your prompt reply. I am aware of the link you provided,
> but it seems they are rather hand-waving. It would be nice if I could be
> dire
Thanks Justin for your prompt reply. I am aware of the link you provided,
but it seems they are rather hand-waving. It would be nice if I could be
directed to a source code of some sort.
Greg
On Sat, Nov 13, 2010 at 11:50 AM, Justin A. Lemkul wrote:
>
>
> Yongchul Chung wrote:
>
Hello gmx-users,
I ran two short simulation in series (simulation A --> simulation B). The
output *.gro file from the simulation A was used as an input file for the
simulation B. If I compare the energy value at the end of simulation A, and
t=0 at simulation B, they are different (<0.1% deviation)
Hello gmx-users,
I ran two short simulation in series (simulation A --> simulation B). The
output *.gro file from the simulation A was used as an input file for the
simulation B. If I compare the energy value at the end of simulation A, and
t=0 at simulation B, they are different (<0.1% deviation)
r GROMACS users
>
> >
> >
> > ----- Original Message -
> > From: Yongchul Chung
> > Date: Thursday, November 4, 2010 10:28
> > Subject: [gmx-users] extending simulation without cpt file
> > To: Discussion list for GROMACS users
> >
> > > Hello
Hello gmxers,
I am using GROMACS 4.0.3. I have original trr, edr, log and tpr file but
erased cpt file. However, I need to extend the simulation from the end of
the trajectory file. I know this will not be binary identical as stated here
(http://www.gromacs.org/Documentation/How-tos/Extending_Simu
Hi,
How big is your file? I assume since you are running 18ps simulation, it
might be big. I remember there's a problem with gromacs not being able to
truncate file size >4Gb.
Greg
On Tue, Sep 7, 2010 at 8:04 AM, David de Sancho wrote:
> Dear Gromacs users
> I am experiencing a problem with
Thanks -- I actually find out a way to do this. Just extract coordinate
information from trajectory file in pdb (for my case, 0ps and 25ns) and
compute displacement by yourself.
Greg
On Wed, Jul 28, 2010 at 6:17 AM, Tsjerk Wassenaar wrote:
> Hi Greg,
>
> So you want a distribution of MSD, right
Hello gmx-users,
I have trajectories which has been obtained from simulating 20,000 atoms in
NVT simulation for 25ns. I recorded the trajectory every 3ps which means
that I have 60,000 data points per atom. I am trying to construct a
histogram where y-axis is the frequency (# of atoms) and x-axis
Dear gmx-users,
I want to construct the Ramachandran Plot for the molecules I am simulating
-- 100 polyethylene chain (n=16). But when I do $ g_rama, I get "Found 0
phi-psi combinations" message. The problem seems to me that when I ran the
simulation initially, I didn't have dihedral information l
On Sun, Oct 25, 2009 at 6:38 PM, Justin A. Lemkul wrote:
>
>
> Yongchul Chung wrote:
>
>> Hello gmx-users,
>>
>> I am running an NPT simulation with 100 molecules of n-alkane and trying
>> to impose uni-axial pressure of these molecules using semiisotropic opt
On Sun, Oct 25, 2009 at 6:28 PM, Mark Abraham wrote:
> Yongchul Chung wrote:
>
>> Hello gmx-users,
>>
>> I am running an NPT simulation with 100 molecules of n-alkane and trying
>> to impose uni-axial pressure of these molecules using semiisotropic option
>> i
Hello gmx-users,
I am running an NPT simulation with 100 molecules of n-alkane and trying to
impose uni-axial pressure of these molecules using semiisotropic option in
grompp.mdp.
However, as the box seems to distort significantly due to the imposed
pressure which leads to the following error mess
I jumped to the conclusion too fast. Thanks Justin for correcting me.
Disregard my previous comment please.
On Tue, Oct 13, 2009 at 10:35 PM, Justin A. Lemkul wrote:
>
>
> Yongchul Chung wrote:
>
>> I think your box is too small. try changing them.
>>
>>
> What
I think your box is too small. try changing them.
On Tue, Oct 13, 2009 at 8:05 PM, Justin A. Lemkul wrote:
>
>
> Nilesh Dhumal wrote:
>
>> Hello,
>>
>> I am trying to equilibrate glucose in water using Gromacs
>> 4.0.5 version. I am geting the error immidiately after the mdrun starts
>> Warning
The experimental value of the compressibility of n-alkanes, DMS, and
1-alcohols can be found in following reference document.
http://www.rsc.org/publishing/journals/CP/article.asp?doi=b206425a
On Tue, Oct 13, 2009 at 4:08 PM, Justin A. Lemkul wrote:
>
>
> Pan Wu wrote:
>
>> Hello everyone,
>>
ditto. I hope they are upgrading the server.
On Tue, Oct 13, 2009 at 11:29 AM, Michael Shirts wrote:
> I'm getting:
>
> Site settings could not be loaded
>
> We were unable to locate the API to request site settings. Please see
> below for debugging information.
>
> HTTP Response Status Code: 50
.
On Fri, Oct 9, 2009 at 11:22 AM, Justin A. Lemkul wrote:
>
>
> Yongchul Chung wrote:
>
>> yes I carried out energy minimization and used following parameters.
>>
>>
> OK, so what values of potential energy and maximum force did EM achieve?
>
> -Justin
0.01
>
> You are using a 10 fs timestep!!! That is way too long. Standard is 2 (with
> bond constraints).
>
>
>
> Yongchul Chung wrote:
>
>> Hi all,
>>
>> I am trying to simulate 100 molecules of n-alkane molecules but keep
>> receiving LINC errors.
&
Hi all,
I am trying to simulate 100 molecules of n-alkane molecules but keep
receiving LINC errors.
When I completed steepest descent I received following msg:
Steepest Descents converged to Fmax < 500 in 819 steps
Potential Energy = 1.7174361e+05
Maximum force = 4.4903098e+02 on atom 172
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