Dear Dr.Justin
I had the same problem.
I modified the charges and charge groupsin the topology of a drug.the net
charge of it is zero(I am sure)
though,when I used pdb2gmx it resulted a NOTE like the following:
NOTE:The system has non-zero total charge: 3.03e00
I continued simulation and
Dear Dr.Justin
What can we do (how can neutralize system) if the total charge of our system
was not integer?
I think there is not any solution and we have to simulate a charged system
not a neutral.
Am I right?
Thanks in advance
On Wed, Apr 6, 2011 at 11:12 AM, mohsen ramezanpour
On 6/04/2011 2:51 PM, Peter C. Lai wrote:
Hello
I am constructing a ligand for which I wish to use the new Charmm CGenFF
parameters (a long aliphatic ketone).
I am using Tom/Par's charmm36 lipid conversion as a baseline template for
comparison:
For reference, c36 lipid CTL3 atoms (in the case
On 6/04/2011 4:42 PM, mohsen ramezanpour wrote:
Dear Dr.Justin
I had the same problem.
I modified the charges and charge groupsin the topology of a drug.the
net charge of it is zero(I am sure)
though,when I used pdb2gmx it resulted a NOTE like the following:
NOTE:The system has non-zero
On 6/04/2011 4:45 PM, mohsen ramezanpour wrote:
Dear Dr.Justin
What can we do (how can neutralize system) if the total charge of our
system was not integer?
I think there is not any solution and we have to simulate a charged
system not a neutral.
Am I right?
I suspect every tutorial for
Daer Dr.Mark
You are right,But all of them(as I know) have integer charges!
the problem is simullating a system with partial charges.
We absolutely have such systems.
On Wed, Apr 6, 2011 at 11:22 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 6/04/2011 4:45 PM, mohsen ramezanpour wrote:
On 06/04/11, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote:
Daer Dr.Mark
You are right,But all of them(as I know) have integer charges!
the problem is simullating a system with partial charges.
We absolutely have such systems.
Read the other link I provided. 3.03e00 indicates
Hi,
No we don't. You can't have fractions of elementary particles in your
molecules.
Erik
mohsen ramezanpour skrev 2011-04-06 09.13:
Daer Dr.Mark
You are right,But all of them(as I know) have integer charges!
the problem is simullating a system with partial charges.
We absolutely have such
Thank you.
I read it and I understood your mean.
On Wed, Apr 6, 2011 at 11:52 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 06/04/11, *mohsen ramezanpour * ramezanpour.moh...@gmail.com wrote:
Daer Dr.Mark
You are right,But all of them(as I know) have integer charges!
the problem is
On Wed, Apr 6, 2011 at 11:53 AM, Erik Marklund er...@xray.bmc.uu.se wrote:
Hi,
No we don't. You can't have fractions of elementary particles in your
molecules.
Dear Erik
Yes,You are right.It is obvious .
But I wanted to simulate a part of my system.for example a part of my
protein!
I was
On 6/04/2011 3:54 PM, Tom Dupree wrote:
Greetings all,
I am trying to learn/use GROMACS for evaluating ligand dockings.
After some effort I managed to get a run through EM, equilibration and
production with protein and water.
I am now having some difficulty getting a similar run going with a
mohsen ramezanpour skrev 2011-04-06 09.31:
On Wed, Apr 6, 2011 at 11:53 AM, Erik Marklund er...@xray.bmc.uu.se
mailto:er...@xray.bmc.uu.se wrote:
Hi,
No we don't. You can't have fractions of elementary particles in
your molecules.
Dear Erik
Yes,You are right.It is obvious .
Yes, Mark is exactly correct about the glitch. I had just forgotten to
change this default charge in the ffnonbonded.itp when copying from
another atom. As mentioned this has no impact as these charges are never
used by pdb2gmx.
Cheers
Tom
Mark Abraham wrote:
On 6/04/2011 2:51 PM, Peter C.
Dear All,
I would like to perform some MD of disaccharides in water using GROMACS and the
new ff for sugars GROMOS45ACARBO from Hansen and unenberger(JCC, 32, 6, 2011).
Does somebody have these parameters in the GROMACS format (e.g. the *.itp
files) and want to share them with me.
Thank
On 2011-04-06 01:49:50AM -0500, Mark Abraham wrote:
The standard CHARMM .prm files give an indication of how the parameters
will be used, so it's just a matter of converting units and taking care
of any constants.
Looks like if I use
hm...
is it possible that there is partial charge because of terminal of zwitterions?
(NH3+ and COO-)
When i tried to make system with terminal of just NH3+ and COO-, there was no
partial charge like 5.00.
But when i used zwitterion terminal, that made the 5.05 charge of the system..
it can be
Hyunsik wrote:
hm...
is it possible that there is partial charge because of terminal of
zwitterions?
(NH3+ and COO-)
When i tried to make system with terminal of just NH3+ and COO-, there
was no partial charge like 5.00.
But when i used zwitterion terminal, that made the 5.05 charge of
Thank you for your help.
But if you don't mind can you tell me more specifically?
Actually I don't know exactly what isolated protein system is.
hyun
2011. 4. 6., 오후 8:56, Justin A. Lemkul 작성:
Hyunsik wrote:
hm...
is it possible that there is partial charge because of terminal of
On 6/04/2011 10:03 PM, Hyunsik wrote:
Thank you for your help.
But if you don't mind can you tell me more specifically?
Actually I don't know exactly what isolated protein system is.
The zwitterion option should only be used for a polypeptide of exactly
one residue, whose termini should be
Hyunsik wrote:
Thank you for your help.
But if you don't mind can you tell me more specifically?
Actually I don't know exactly what isolated protein system is.
If you're running pdb2gmx on a single amino acid, then some force fields have
special parameters for this zwitterion. If you
Dear All
I used mdrun for generating NVT
It crashed and massage was:
Trying to get md5sum: nvt-1.trr: Stale NFS file handle
Trying to get md5sum: nvt-1.edr: Stale NFS file handle
---
Program mdrun, VERSION 4.5.3-dev-20110310-a52f8-dirty
oh.. i have missed it ...
Thank you, Justin and Mark.
it's really helpful for me.
Hyun
2011. 4. 6., 오후 9:16, Justin A. Lemkul 작성:
Hyunsik wrote:
Thank you for your help.
But if you don't mind can you tell me more specifically?
Actually I don't know exactly what isolated protein
Dear All
I used again grompp and then mdrun with the same commands,
they run successfuluy!!
of course with the same error.
I copy and paste the command shell when these are completed:
Program mdrun, VERSION 4.5.3-dev-20110310-a52f8-dirty
Source code file:
On 6/04/2011 10:29 PM, mohsen ramezanpour wrote:
Dear All
I used mdrun for generating NVT
It crashed and massage was:
Trying to get md5sum: nvt-1.trr: Stale NFS file handle
You have an intermittent problem with your Network File System. For some
reason GROMACS can't keep writing to the same
I followed your suggestions and i tried to perform a MD run wit GROMACS and
NAMD for dialanine peptide in a water box. The cell side cubic box was 40 A.
GROMACS:
With the free energy module there is a drop in gromacs performance of about
10/20 fold.
Standard MD: Time: 6.693
Dear All,
I need to hack mdrun in rather complex way and need some help from people, who
understand Gromacs internals really well.
My problem is the following. Each N MD steps I want to pass current coordinates
and forces to custom function, which transforms them in a certain way (doesn't
Dear all,
I am trying to optimize runtimes/speed for a series of
calculations i plan to do with a rather complex system.
When looking at runtimes I observed one peculiar issue:
the estimated runtime written to stderr by mdrun with the -v
option keepsgrowing ... in my experience this estimate
Hi,
This doesn't sound like normal behavior. In fact, this is not what I
typically observe. While there may be a small performance difference,
it is probably at the level of a few percent. Certainly not a factor
of more than 10.
You may want to provide an mdp file and topology, etc. so someone
Michael Brunsteiner wrote:
Dear all,
I am trying to optimize runtimes/speed for a series of
calculations i plan to do with a rather complex system.
When looking at runtimes I observed one peculiar issue:
the estimated runtime written to stderr by mdrun with the -v
option keepsgrowing ... in
David Mobley wrote:
Hi,
This doesn't sound like normal behavior. In fact, this is not what I
typically observe. While there may be a small performance difference,
it is probably at the level of a few percent. Certainly not a factor
of more than 10.
I see about a 50% reduction in speed when
Hi,
As Justin said, it's probably the imbalance which is causing the
slowdown. You can take a look at the statistics at the end of the log
file. One simple thing you could do is to compare the log file of your
long, gradually slowing down run with a shorter run to see which part
takes more time.
Dear Dr.Justin
I had asked this question before but unfortunately I didn't answered good!
Instead of Pulling and separating some structures in definite distances,
I located my drug in definite distances along z axis (as my initial
structures for doing umbrella sampling).
Am I right?
The main
I posted my test files in:
https://www.dropbox.com/link/17.-sUcJyMeEL?k=0f3b6fa098389405e7e15c886dcc83c1
This is a run for a dialanine peptide in a water box.
The cell side cubic box was 40 A.
The directory is organized as :
TEST\
topol.top
Run-00/confout.gro; Equilibrated
mohsen ramezanpour wrote:
Dear Dr.Justin
I had asked this question before but unfortunately I didn't answered good!
Instead of Pulling and separating some structures in definite distances,
I located my drug in definite distances along z axis (as my initial
structures for doing umbrella
shivangi nangia wrote:
Hello,
I am having problems in carrying out a NPT equilibration of my system at
500 K.
System: A 5 nm cube with peptide, Li+ ions and 2,5-dihydroxybenzoic acid
anion.
NVT equilibration gives expected results.
When I load the npt.gro file in VMD, its seems as if
I am trying to use g_bar to derive a PMF curve from non-equilibrium
trajectory data. I am using v 4.5.4 on a Mac running OSX 10.6.7.
I am using the end-to-end distance of a peptide as the co-ordinate of
interest. After doing a long simulation of the peptide, I selected the frames
Warren Gallin wrote:
I am trying to use g_bar to derive a PMF curve from non-equilibrium
trajectory data. I am using v 4.5.4 on a Mac running OSX 10.6.7.
I am using the end-to-end distance of a peptide as the co-ordinate of
interest. After doing a long simulation of the peptide, I selected
I am having problems in carrying out a NPT equilibration of my system at 500
K.
System: A 5 nm cube with peptide, Li+ ions and 2,5-dihydroxybenzoic acid
anion.
NVT equilibration gives expected results.
When I load the npt.gro file in VMD, its seems as if the molecules have
On 2011-04-06, at 10:58 AM, Justin A. Lemkul wrote:
Warren Gallin wrote:
I am trying to use g_bar to derive a PMF curve from non-equilibrium
trajectory data. I am using v 4.5.4 on a Mac running OSX 10.6.7.
I am using the end-to-end distance of a peptide as the co-ordinate of
interest.
Warren Gallin wrote:
On 2011-04-06, at 10:58 AM, Justin A. Lemkul wrote:
Warren Gallin wrote:
I am trying to use g_bar to derive a PMF curve from non-equilibrium
trajectory data. I am using v 4.5.4 on a Mac running OSX 10.6.7.
I am using the end-to-end distance of a peptide as the
Hello Justin,
Several days ago you answered my question about calculating nonbonded terms:
Question: If I want to look at nonboded interactions only, do I have to add
Coul. recip. to [ LJ (SR) + Coulomb (SR) ] ?
Answer: The PME-related terms contain both solute-solvent, solvent-solvent,
and
Elisabeth wrote:
Hello Justin,
Several days ago you answered my question about calculating nonbonded
terms:
Question: If I want to look at nonboded interactions only, do I have to
add Coul. recip. to [ LJ (SR) + Coulomb (SR) ] ?
Answer: The PME-related terms contain both
Elisabeth,
You CAN, in fact calculate the contribution of the reciprocal part
of the PME energy to the binding energy between two components in
a heterogeneous system, its just quite tedious...
say, your system is molecules A and B for which you want to know
the interaction energy, and the rest
dear Justin A. Lemkul,
thanks for your reply. You were right. Now, it works and generates the
nitrogen box. But when I type:
grompp_d -f ions.mdp -c 3INC_solv.gro -p topol.top -o ions.tpr
I recieve this error: source file: grompp.c, line: 362
number of coordinates in coordinate file
sarah k wrote:
dear Justin A. Lemkul,
thanks for your reply. You were right. Now, it works and generates the
nitrogen box. But when I type:
grompp_d -f ions.mdp -c 3INC_solv.gro -p topol.top -o ions.tpr
I recieve this error: source file: grompp.c, line: 362
number of coordinates in
Hello all:
I need to calculate stress autocorrelation function for my polymeric system. Is
there a way to calculate this using gromacs tools?
Thanks,
SN
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
On 6 April 2011 15:01, Michael Brunsteiner mbx0...@yahoo.com wrote:
Elisabeth,
You CAN, in fact calculate the contribution of the reciprocal part
of the PME energy to the binding energy between two components in
a heterogeneous system, its just quite tedious...
say, your system is
Elisabeth wrote:
On 6 April 2011 15:01, Michael Brunsteiner mbx0...@yahoo.com
mailto:mbx0...@yahoo.com wrote:
Elisabeth,
You CAN, in fact calculate the contribution of the reciprocal part
of the PME energy to the binding energy between two components in
a heterogeneous
On 6 April 2011 19:28, Justin A. Lemkul jalem...@vt.edu wrote:
Elisabeth wrote:
On 6 April 2011 15:01, Michael Brunsteiner mbx0...@yahoo.com mailto:
mbx0...@yahoo.com wrote:
Elisabeth,
You CAN, in fact calculate the contribution of the reciprocal part
of the PME energy to
Elisabeth wrote:
On 6 April 2011 19:28, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Elisabeth wrote:
On 6 April 2011 15:01, Michael Brunsteiner mbx0...@yahoo.com
mailto:mbx0...@yahoo.com mailto:mbx0...@yahoo.com
mailto:mbx0...@yahoo.com
On 7/04/2011 9:23 AM, Elisabeth wrote:
On 6 April 2011 15:01, Michael Brunsteiner mbx0...@yahoo.com
mailto:mbx0...@yahoo.com wrote:
Elisabeth,
You CAN, in fact calculate the contribution of the reciprocal part
of the PME energy to the binding energy between two components in
Dear all,
I am now trying to simulate crystals in Gromacs.
What I did was to convert the original crystal structure in cif format
to pdb format and then use genconf to replicate the cells and run MD.
Is it proper to do it in this way? Because the structure I got after MD
run was
On 7/04/2011 1:55 PM, ZHANG Lu wrote:
Dear all,
I am now trying to simulate crystals in Gromacs.
What I did was to convert the original crystal structure in cif format
to pdb format and then use genconf to replicate the cells and run MD.
Is it proper to do it in this way?
It's
Dear all,
I'm using a c++ code to handle the xtc file with 'xtcio.h', but get the
error when executing it.
the command I use:
g++ test.cpp -o test -I/usr/local/gromacs/include/gromacs
-L/usr/local/gromacs/lib -lgmx
./test
Error:
./test: error while loading shared libraries:
Ok I'm now getting the dreaded Unknown bond_atomtype CG2O5
grompp fatal error. I ran pdb2gmx on a pdb of my ligand and it generated
a gro and a top file:
http://pastebin.com/HL3k7EPU for the gro
http://pastebin.com/y6T4ir7y for the top
I ran grompp -f em.mdp -c nonanone.gro -p nonanone.top -o
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