Lennard-Jones PME is planned for 5.0
Mark
On Aug 28, 2013 8:36 AM, "Gianluca Interlandi"
wrote:
> Hi!
>
> Just wondering whether gromacs has (or plans to implement) a correction
> for the loss of long range LJ interactons? Something similar to
> LJcorrection in NAMD or IPS in CHARMM.
>
> Thanks!
It can be. Lack of explicit degrees of freedom of solvent can make
achieving equipartition tricky. With CHARMM27 and virtual sites in implicit
solvent, I have sometimes found it necessary to use a sub-femtosecond time
step at the start of equilibration, even where there were no atomic
clashes. Mayb
Hi,
What is LJ PME? I googled it and got this publication?
http://pubs.acs.org/doi/abs/10.1021/ct400146w
So, LJ will not be cut off at some r, but you will have a real+fourier part
similar to electrostatics. Is that LJ PME? What are the advantages?
On Wed, Aug 28, 2013 at 12:36 PM, Mark Abraham
On 2013-08-28 09:31, rajat desikan wrote:
Hi,
What is LJ PME? I googled it and got this publication?
http://pubs.acs.org/doi/abs/10.1021/ct400146w
So, LJ will not be cut off at some r, but you will have a real+fourier part
similar to electrostatics. Is that LJ PME? What are the advantages?
htt
Secondarily, one could use the same cut-off for LJ and electrostatics,
and treat their respective lattice components however you like. This
simplifies implementations for computing short-ranged interactions,
while facilitating iso-accuracy load balancing across heterogeneous
compute units.
Mark
O
Hi Dear Gromacs users,
I have a question about the total charge of a system. I executed pdb2gmx
command which the result is quited below:
"Keeping all generated dihedrals
Making cmap torsions...There are 7808 dihedrals, 591 impropers, 5298 angles
7596 pairs, 2922 bonds and 0 vi
If you're not sure what charge your chains should have had, then you
should go back and think about the titratable residues and what you're
trying to model. Don't assume some code's defaults are what you want!
The earlier mention of "total charge -3" refers to one of the chains,
but pdb2gmx is not
Hello,
At NPT stage the two leaflets in DMPC bilayer is separated a while and comes
closer. Is this common in this stage or any thing goes wrong in
equillibration.
Thanks
--Rama
--
View this message in context:
http://gromacs.5086.x6.nabble.com/DMPC-Bilayer-tp5010783.html
Sent from the GROM
On 8/28/13 11:12 AM, Rama wrote:
Hello,
At NPT stage the two leaflets in DMPC bilayer is separated a while and comes
closer. Is this common in this stage or any thing goes wrong in
equillibration.
Depending on what the previous preparation steps were, this can certainly occur.
-Justin
--
Hello:
I am constraining one part of the protein and trying to generate md.tpr
with command:
grompp -f md.mdp -c npt4.gro -n -o md.tpr
it works fine in 4.6.3, but it failed in 4.5.5 with following warning
messages:
WARNING 1 [file md.mdp, line 65]:
Unknown left-hand 'cutoff-scheme' in p
Hello:
I am trying to use following command to run 4.6.3 in a HPC cluster:
mpiexec -n 32 /opt/gromacs/4.6.3/bin/mdrun_mpi -dlb yes -v -s md.tpr -x
md.xtc -o md.trr -g md.log -e md.edr >& md.info
the 4.5.5 works fine in this machine with command:
mpiexec -n 32 mdrun -nosum -dlb yes -v -s m
On 8/28/13 12:39 PM, Albert wrote:
Hello:
I am trying to use following command to run 4.6.3 in a HPC cluster:
mpiexec -n 32 /opt/gromacs/4.6.3/bin/mdrun_mpi -dlb yes -v -s md.tpr -x md.xtc
-o md.trr -g md.log -e md.edr >& md.info
the 4.5.5 works fine in this machine with command:
mpiexe
On 8/28/13 11:48 AM, Albert wrote:
Hello:
I am constraining one part of the protein and trying to generate md.tpr with
command:
grompp -f md.mdp -c npt4.gro -n -o md.tpr
it works fine in 4.6.3, but it failed in 4.5.5 with following warning messages:
WARNING 1 [file md.mdp, line 65]:
Unk
On 08/28/2013 07:07 PM, Justin Lemkul wrote:
WARNING 2 [file helix.itp, line 1]:
Too few parameters on line (source file toppush.c, line 1501)
Looks concerning - what's line 1?
here is the initial lines:
; position restraints for part of C-alpha of Protein
[ position_restraints ]
; i fun
On 8/28/13 1:21 PM, Albert wrote:
On 08/28/2013 07:07 PM, Justin Lemkul wrote:
WARNING 2 [file helix.itp, line 1]:
Too few parameters on line (source file toppush.c, line 1501)
Looks concerning - what's line 1?
here is the initial lines:
; position restraints for part of C-alpha of Prot
On 08/28/2013 07:25 PM, Justin Lemkul wrote:
Looks normal, so without context of how it is #included, there's not
much to diagnose here.
here is my #include in topol.top file:
; Include Position restraint file
#ifdef POSRES
#include "restrain.itp"
#endif
I first generate restrain for all
On 8/28/13 1:36 PM, Albert wrote:
On 08/28/2013 07:25 PM, Justin Lemkul wrote:
Looks normal, so without context of how it is #included, there's not much to
diagnose here.
here is my #include in topol.top file:
; Include Position restraint file
#ifdef POSRES
#include "restrain.itp"
#endif
On 08/28/2013 07:38 PM, Justin Lemkul wrote:
That's not the problem. It's complaining about whatever is on line 1
(not clear from the previous message if the comment line is #1 or a
blank line), so assuming that the #ifdef is in the right place
(probably is, or the error would be different),
On Wed, Aug 28, 2013 at 7:06 PM, Justin Lemkul wrote:
>
>
> On 8/28/13 12:39 PM, Albert wrote:
>>
>> Hello:
>>
>> I am trying to use following command to run 4.6.3 in a HPC cluster:
>>
>> mpiexec -n 32 /opt/gromacs/4.6.3/bin/mdrun_mpi -dlb yes -v -s md.tpr -x
>> md.xtc
>> -o md.trr -g md.log -e
Thanks for your replies, Mark. What do you think about the current
DispCorr option in gromacs? Is it worth it trying it? Also, I wonder
whether using DispCorr for LJ + PME for Cb justifies reducing the cutoff
for non-bonded to 1 nm with the CHARMM force field, where 1.2 nm is
usually recommende
On 8/28/13 7:28 PM, Gianluca Interlandi wrote:
Thanks for your replies, Mark. What do you think about the current DispCorr
option in gromacs? Is it worth it trying it? Also, I wonder whether using
DispCorr for LJ + PME for Cb justifies reducing the cutoff for non-bonded to 1
nm with the CHARMM
Hello everyone,
I want to use CGennFF force field in GROMACS. I downloaded the Cgenffbon.itp
and Cgenffnb.itp files and I put them in charmm36.ff directory.
- I replaced the lines in the forcefield.itp to #include "Cgenffbon.itp" and
#include "Cgenffnb.itp"
- I modified the rtp file and I i
On 8/28/13 8:23 PM, Golshan Hejazi wrote:
Hello everyone,
I want to use CGennFF force field in GROMACS. I downloaded the Cgenffbon.itp
and Cgenffnb.itp files and I put them in charmm36.ff directory.
- I replaced the lines in the forcefield.itp to #include "Cgenffbon.itp" and #include
"Cge
Current CHARMM development relies on a 1.2-nm cutoff for LJ, so that's
how we balance all of the forces during parameterization.
Ok, I agree. What about the use of PME for Coulomb? The CHARMM PARAM22
force field was parametrized using SHIFT on electrostatic forces making it
zero after 12 A (pl
On 8/28/13 9:09 PM, Gianluca Interlandi wrote:
Current CHARMM development relies on a 1.2-nm cutoff for LJ, so that's how we
balance all of the forces during parameterization.
Ok, I agree. What about the use of PME for Coulomb? The CHARMM PARAM22 force
field was parametrized using SHIFT on el
Justin,
I respect your opinion on this. However, in the paper indicated below by
BR Brooks they used a cutoff of 10 A on LJ when testing IPS in CHARMM:
Title: Pressure-based long-range correction for Lennard-Jones interactions
in molecular dynamics simulations: Application to alkanes and inte
Dear Gromacs ,
I running the md simulation for protein complex (44 kd ) with amber99sb-ildn
force filed . iam getting error as follows , looks like it is syntax error .
Input file: gmx-495644.pdb Base name: gmx-495644 Source directory:
/scratch/home/enmr028/home_cream_840250368/CREAM840250368 GR
Hi,
I ran some MD simulations (NPT ensemble) and a series of simulations
to determine the free energy of water solvation of a not to big
molecule.
I noticed that while I was able to run the MD simulations using all
the CPUs (or threads) in my workstation (12 CPUs or 24 threads,
respectively),
hello Mark:
thanks a lot for kind advices. Here is my log file for output of mdrun
-version, There are always some duplicate informations and files
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdrun_mpi
Program: mdru
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