Hi, Justin,
You are right, I should first fix the bad geometry.
I check 1dx0.pdb, and the problematic areas are:
atom1 atom2
1 N1+ (GLY124 N) 4 H (GLY124 HT3)
181 C (PRO137 CD)182 H (PRO137 HD1)
262 H (PHE14
OK I found the problem. I had installed Surfnet the protein cavity finder a
few weeks ago, and it turns out this also has a function called genbox! so
my silly mistake.
I was wondering why centre and not center.
Thanks,
Matt
On Mon, Jun 10, 2013 at 6:23 PM, Justin Lemkul [via GROMACS] <
ml-
On 6/11/13 4:12 PM, Steven Neumann wrote:
Dear Gromacs Users,
I got really confused: In manual [defualts ]:
"nbfunc is the non-bonded function type. Use 1 (Lennard-Jones) or 2
(Buckingham)"
I want to use mdrun -table table.xvg with my own potential, which one I
should choose?
"gen-pairs - i
On 6/11/13 3:47 PM, Steven Neumann wrote:
Thank you Justin. So using nrexcl 0 or 1 (should be the same with
constraints) and type 1 will allow bonded atoms to interact (vdW) with each
other?
No, there will be differences for type 1 in this case. Type 1 generates
exclusions per nrexcl. Usi
Note that this works fine with 4.5.5.
when I installed using:
./configure CPPFLAGS="-I/home/kaushik/fftw-new/include"
LDFLAGS="-L/home/kaushik/fftw-new/lib" --enable-mpi --prefix
/home/kaushik/gromacs_executable/gromacs-old
ldd mdrun on the 4.5.5 version correctly points to the fftw and the mpi
If you only want the total for the system or a delta for an entire run, indexed group there of, covarience (covar/aneig) does a good job. I found neither actually fit, but the covarience does, or if you do it by hand using only LJ parmeters for the indexed sets, however I was using proteins, so f
> >or should i be doing < U+*ref_p > = ?
>More specifically, + *ref_p = H
> isn't really meaningful thing. I mean, you can define something
>such that = H, but that's not really thermodynamics.
sorry I always have issues deciding how to talk about this stuff, so thanks
for putting up with
Hi Amil,
On Mon, Jun 10, 2013 at 11:03 PM, Amil Anderson
wrote:
> Szilárd,
>
> I tried the build using a PATH without the Intel compilers and NOT including
> the directives -DGMX_EXTERNAL_BLAS=OFF and -DGMX_EXTERNAL_LAPACK=OFF and it
> used the FFTW 3.2 wrappers to MKL. Here is the output fro
> or should i be doing < U+*ref_p > = ?
More specifically, + *ref_p = H
isn't really meaningful thing. I mean, you can define something
such that = H, but that's not really thermodynamics.
> example system gives = -1168 kJ/mol and i find = -725 kJ/mol either
Interesting. What material at
>You should not use pV from g_energy though, as Michael explained, rather
>you need ref_p times . This precludes that your system is in
>equilibrium of course.
That is what I had initially thought, then take that with the to get
?
or should i be doing < U+*ref_p > = ?
But even so I still get d
On 2013-06-11 21:57, Jeffery Perkins wrote:
If you are computing enthaply in the NPT ensemble, P is constant, and
is the applied pressure.
The "pressure" quantity calculated from the KE and the virial is not
the pressure. It is a quantity that when averaged over time is equal
the pressure. O
Dear Gromacs Users,
I got really confused: In manual [defualts ]:
"nbfunc is the non-bonded function type. Use 1 (Lennard-Jones) or 2
(Buckingham)"
I want to use mdrun -table table.xvg with my own potential, which one I
should choose?
"gen-pairs - is for pair generation. The default is ‘no’, i.
>If you are computing enthaply in the NPT ensemble, P is constant, and
>is the applied pressure.
>The "pressure" quantity calculated from the KE and the virial is not
>the pressure. It is a quantity that when averaged over time is equal
>the pressure. Only the average is meaningful macroscop
Thank you Justin. So using nrexcl 0 or 1 (should be the same with
constraints) and type 1 will allow bonded atoms to interact (vdW) with each
other?
On Tue, Jun 11, 2013 at 6:10 PM, Justin Lemkul wrote:
>
>
> On 6/11/13 10:46 AM, Steven Neumann wrote:
>
>> I was not sure about the fucntion type
Dear GROMACS users list members:
We are pleased to announce the 2013 GROMACS USA Workshop and
Conference at the University of Virginia in Charlottesville, Virginia,
on September 13-15th. This will be the first full GROMACS workshop
held here in the U.S.
The workshop and conference will consist o
If you are computing enthaply in the NPT ensemble, P is constant, and
is the applied pressure.
The "pressure" quantity calculated from the KE and the virial is not
the pressure. It is a quantity that when averaged over time is equal
the pressure. Only the average is meaningful macroscopically.
that's what i thought, and what i tried to do, my pressure is a bit higher
then that, we want a Lennard-Jones liquid so it's running at 1000+ bar, and
while I agree that gromacs is giving H as Etot + pV it appears that when i
calculate pV i get a different value from what g_energy returns for it I
On 2013-06-11 20:09, Jeffery Perkins wrote:
This may just be me not understanding what I'm looking at, but I'm trying to
get the Enthalpy of a simple test system of LJ fluid, running version 4.5.4
initially I've tried using the enthalpy option in g_energy but I noticed
that if i compare that valu
Thanks, I must have confused the units for the simulated annealing
parameters.
On Tue, Jun 11, 2013 at 2:12 PM, Dr. Vitaly Chaban wrote:
> According to your MD parameters, your system should attain T=300K at the
> 300th
> nanosecond.
>
> Since you have run only for 50 * 0.002 ps = 1ns, you g
According to your MD parameters, your system should attain T=300K at the 300th
nanosecond.
Since you have run only for 50 * 0.002 ps = 1ns, you got T=1K, since
temperature elevates linearly, based on your setup.
Dr. Vitaly Chaban
On Tue, Jun 11, 2013 at 8:07 PM, Marc Hömberger wrote:
>
On 6/11/13 2:07 PM, Marc Hömberger wrote:
Hi,
I have a system setup (minimized etc.) and wanted to heat this system
gradually with simulated annealing. I set up the mdp file as you can see
below (simulated annealing part is marked bold). But when the heating is
finished, the log file tells me
This may just be me not understanding what I'm looking at, but I'm trying to
get the Enthalpy of a simple test system of LJ fluid, running version 4.5.4
initially I've tried using the enthalpy option in g_energy but I noticed
that if i compare that value to H=U+pV using either the average or the
i
Hi,
I have a system setup (minimized etc.) and wanted to heat this system
gradually with simulated annealing. I set up the mdp file as you can see
below (simulated annealing part is marked bold). But when the heating is
finished, the log file tells me that the temperature of the system is only
1K
Hi,
I am using the Martini field for those who wanted to know.
My values for the mdp file for ref_p were inspired from this paper as it
says pressure was coupled anisotropically to 0 bar in all directions.
http://www.sciencedirect.com/science/article/pii/S0005273611002045
I think I will try to
Is there a reason you would like to keep it at 105K? Just curious which
forcefield are you using?
Also, for proper surface tension, there is an option called
pcoupltype = surface-tension.
I think you should check that out.
--
View this message in context:
http://gromacs.5086.x6.nabble.co
On 6/11/13 1:25 PM, Neha wrote:
Hi everybody,
Thank you so much for taking the time to read this.
I thought ref_p would need to be 0.0 and 0.0 if I wanted zero surface
tension. How else could I get a tensionless membrane?
As far as I understand, surface tension is only applied when using "p
Exactly so. I think Gromacs issues a warning when you try to initialize
velocities with Parrinello-Rahman barostat. But if you performed your
equilibration at 105K using Berendsen barostat, I think it should be okay
and you should put gen-vel = no.
--
View this message in context:
http://groma
Hi everybody,
Thank you so much for taking the time to read this.
I thought ref_p would need to be 0.0 and 0.0 if I wanted zero surface
tension. How else could I get a tensionless membrane?
As for the generating velocities, I completely forgot that would ruin the
equilibrium. Would you recommend
On 6/11/13 1:13 PM, HANNIBAL LECTER wrote:
ref_p= 0.0 0.0 ??
Are you sure about this??
That's a likely culprit. See below for another.
On Tue, Jun 11, 2013 at 12:08 PM, Dr. Vitaly Chaban wrote:
what happens to your energy before the observed crash? does the crash
On 6/11/13 10:55 AM, Dr. Vitaly Chaban wrote:
On Tue, Jun 11, 2013 at 3:52 PM, Justin Lemkul mailto:jalem...@vt.edu>> wrote:
On 6/11/13 9:27 AM, Dr. Vitaly Chaban wrote:
This problem indeed happens from time to time. With versions 4.5+ it is
more frequent than with ve
ref_p= 0.0 0.0 ??
Are you sure about this??
On Tue, Jun 11, 2013 at 12:08 PM, Dr. Vitaly Chaban wrote:
> what happens to your energy before the observed crash? does the crash
> happen at the same time-step each time?
>
>
> Dr. Vitaly Chaban
>
>
> On Tue, Jun 11, 2013 at 5:2
On 6/11/13 10:46 AM, Steven Neumann wrote:
I was not sure about the fucntion type (1 or 2). Once in manual it is
stated that function 1 is only for exclusions and another time it can be
used to miimc bonds. Both functions are working though. Thanks anyway.
More precisely, constraints of typ
what happens to your energy before the observed crash? does the crash
happen at the same time-step each time?
Dr. Vitaly Chaban
On Tue, Jun 11, 2013 at 5:22 PM, Neha wrote:
> Hi everybody,
>
> I am trying to simulate a lipid bilayer and wanted to use Parrinello Rahman
> coupling. However, I r
Hi everybody,
I am trying to simulate a lipid bilayer and wanted to use Parrinello Rahman
coupling. However, I read that Parinello-Rahman is not great for
equilibration so I thought I would do a small run using the Berendsen
barostat to decrease the chances of large oscillations. I then used the .
Steven -
I probably know nothing about "function #2", but "function 1" is used just
everywhere. It does constrain intramolecular distances.
Good luck. Vitaly
Dr. Vitaly Chaban
On Tue, Jun 11, 2013 at 4:46 PM, Steven Neumann wrote:
> I was not sure about the fucntion type (1 or 2). Once in ma
On Tue, Jun 11, 2013 at 3:52 PM, Justin Lemkul wrote:
>
>
> On 6/11/13 9:27 AM, Dr. Vitaly Chaban wrote:
>
>> This problem indeed happens from time to time. With versions 4.5+ it is
>> more frequent than with versions up to 4.0.7. It is not always connected
>> to
>> blowing up in the sense of bad
I was not sure about the fucntion type (1 or 2). Once in manual it is
stated that function 1 is only for exclusions and another time it can be
used to miimc bonds. Both functions are working though. Thanks anyway.
Steven
On Tue, Jun 11, 2013 at 2:18 PM, Dr. Vitaly Chaban wrote:
> I think all i
On 6/11/13 9:27 AM, Dr. Vitaly Chaban wrote:
This problem indeed happens from time to time. With versions 4.5+ it is
more frequent than with versions up to 4.0.7. It is not always connected to
blowing up in the sense of bad contacts, positive potential energy, etc.
The more cores you use per jo
I was having issues with my email earlier today, so some things did not go
through. Apologies if this is a multiple post, but I wanted to make sure it got
through, especially since it provides resolution to a very long-running thread:
On 6/11/13 7:46 AM, Shima Arasteh wrote:
I put the outpu
On 6/11/13 9:38 AM, JW Gibbs wrote:
Hi,
As Justin had already suggested, restraints will lead to nasty atomic
clashes. Looking at the gro file you have provided, it seems that the system
is very poorly equilibrated.
I had a similar issue. If the forcefield you are using is accurate enough,
fo
Hi,
As Justin had already suggested, restraints will lead to nasty atomic
clashes. Looking at the gro file you have provided, it seems that the system
is very poorly equilibrated.
I had a similar issue. If the forcefield you are using is accurate enough,
follow the steps as follows:
1. Take th
On Tue, Jun 11, 2013 at 12:52 PM, Justin Lemkul wrote:
>
>
> On 6/11/13 1:11 AM, mu xiaojia wrote:
>
>> Hi guys,
>>
>> I am using simulated annealing for my protein+water+Ion system, I tried to
>> let the system stay at some temperature for a while, e.g.: stay at 600k
>> from 3000ps to 1 ps,
This problem indeed happens from time to time. With versions 4.5+ it is
more frequent than with versions up to 4.0.7. It is not always connected to
blowing up in the sense of bad contacts, positive potential energy, etc.
The more cores you use per job, the more likely this error to appear. The
larg
I think all is correct.
Why are you asking? People normally report problems.
Dr. Vitaly Chaban
On Tue, Jun 11, 2013 at 12:30 PM, Steven Neumann wrote:
> Dear Gmx Users,
>
> I am running CG simulation and I wish my beads to be constraint - one away
> from each other of 0.4 nm. I wan to use
I put the output file of shrinking steps after 32 iterations:
https://jumpshare.com/b/5Y6WUGv7OT1sOFzsrWgN
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Tuesday, June 11, 2013 3:25 PM
Subject: Re: [gmx-us
On 6/11/13 5:59 AM, Steven Neumann wrote:
On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul wrote:
On 6/10/13 8:42 AM, Justin Lemkul wrote:
On 6/10/13 8:40 AM, Steven Neumann wrote:
On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul wrote:
On 6/10/13 8:23 AM, Steven Neumann wrote:
D
On 6/11/13 6:30 AM, Steven Neumann wrote:
Dear Gmx Users,
I am running CG simulation and I wish my beads to be constraint - one away
from each other of 0.4 nm. I wan to use Lincs for this purpose. I do not
have any bonds in my topology or rtp entry. I just add:
[ constraints ]
1 2 1
On 6/11/13 2:05 AM, Shima Arasteh wrote:
These are the all commands to do iteration:
After generating topology
-concatenate the protein and bilayer structure files:
#cat dimer-newbox.gro popc-whole.gro > system.gro
( Remove unnecessary lines and update the second line of the c
On 6/11/13 1:30 AM, Souilem Safa wrote:
Dear Gromacs users,
I tried to do the simulation of a single molecule in cyclohexane, I'm using
gromos 53a6 force field for both molecules.
i did all the minimization steps. After npt, I runned for 25 000 000 steps.
just after around 100 000 steps, the
On 6/11/13 1:11 AM, mu xiaojia wrote:
Hi guys,
I am using simulated annealing for my protein+water+Ion system, I tried to
let the system stay at some temperature for a while, e.g.: stay at 600k
from 3000ps to 1 ps, then gradually cool it down to 298k, so my mdp is
like:
annealing_time = 0
Dear Gmx Users,
I am running CG simulation and I wish my beads to be constraint - one away
from each other of 0.4 nm. I wan to use Lincs for this purpose. I do not
have any bonds in my topology or rtp entry. I just add:
[ constraints ]
1 2 1 0.4
2 3 1 0.4
...
31 32
Dear Gromacs users,
I tried to do the simulation of a single molecule in cyclohexane, I'm using
gromos 53a6 force field for both molecules.
i did all the minimization steps. After npt, I runned for 25 000 000 steps.
just after around 100 000 steps, the system stops and i got this fatal
error:
Fa
On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul wrote:
>
>
> On 6/10/13 8:42 AM, Justin Lemkul wrote:
>
>>
>>
>> On 6/10/13 8:40 AM, Steven Neumann wrote:
>>
>>> On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul wrote:
>>>
>>>
On 6/10/13 8:23 AM, Steven Neumann wrote:
Dear Gmx U
It is *desirable*.
In many cases of free energy calculations, single precision is still
reliable.
Dr. Vitaly Chaban
On Tue, Jun 11, 2013 at 7:35 AM, Albert wrote:
> Hello :
>
> I am going to use Gromacs with PLUMD plugin to perform Metadynamics.
> Since this methods involved in free ener
Not directly. Code that permitted doing so during the actual simulation
would be far too inefficient. You can use tpbconv and trjconv to make
matching subsets of your .tpr and output trajectory, and pass those through
mdrun -rerun. Or, depending what you actually want, you may need to make an
.mdp
HI Mark:
thank you for kind reply. I found the following in the documentations:
Installations:
Example.
This is the procedure for compiling the serial version of GROMACS, using
the GNU compilers.
tar zxf gromacs-4.0.5.tar.gz
cd gromacs-4.0.5
export plumedir="PLUMED root"
cp $plumedir/patches
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