Hi,
That's definitely a bug and we would like to fix it. Can you please open an
issue at https://redmine.gromacs.org and provide enough information to
reproduce the issue (e.g. tpr files, preferably for a small part of your
replica scheme)?
Mark
On Sun, Nov 5, 2017 at 8:14 AM Daniel Kozuch wrot
On 11/8/17 8:59 PM, Amali Guruge wrote:
Dear Dr. Justin,
Thank you very much for the reply. If I keep the 0.005 as the time step,
what steps should be followed in-order to avoid the LINCS warnings?
Appreciate if you can comment on this.
I already suggested the only two appropriate methods fo
Hi,
As you have learned, such boundary conditions are only available in the
group scheme, the boundary conditions restrict the number of ranks usable,
and the group scheme prevents OpenMP parallelism being useful. We hope to
relax this in future, but your current options are to run slowly, use
dif
Dear Justin,
I tried using OpenMP parallelization with the following command:
mdrun -ntmpi 1 -ntomp 1
which works fine, but if ntomp is increased, I get the below error:-
*OpenMP threads have been requested with cut-off scheme group, but these
are only supported with cut-off scheme verlet*
Is
Dear Dr. Justin,
Thank you very much for the reply. If I keep the 0.005 as the time step,
what steps should be followed in-order to avoid the LINCS warnings?
Appreciate if you can comment on this.
Thank you.
On Thu, Nov 9, 2017 at 12:46 PM, Justin Lemkul wrote:
>
>
> On 11/8/17 8:45 PM, Amali
On 11/8/17 8:45 PM, Amali Guruge wrote:
Dear Gromacs users,
I did energy minimization step and started the equilibration run. However,
when I changed the time step 0.002 to to 0.005, it gave an error; Too many
LINCS warnings. What could be the reason for this? The simulation was
worked without
Dear Gromacs users,
I did energy minimization step and started the equilibration run. However,
when I changed the time step 0.002 to to 0.005, it gave an error; Too many
LINCS warnings. What could be the reason for this? The simulation was
worked without an error until I changed the time step. App
Okay, same thing with 0.5V/nm. I think it's fairly safe to say that there's
something wrong here...
Alex
On Wed, Nov 8, 2017 at 12:25 PM, Alex wrote:
> Good question. Dielectric breakdown of water is generally poorly
> understood and the threshold depends on the ionic strength, but 0.4-0.5V/nm
Good question. Dielectric breakdown of water is generally poorly understood
and the threshold depends on the ionic strength, but 0.4-0.5V/nm is
generally where the fun begins. MD modelers working with solvated systems
casually ignore this, unless they have the great misfortune of getting me
as a re
Thank you Prof. David for your reply and sorry for the late response. So,
now do I have to use the original traj.xtc or still I need to do least
square fitting w.r.t the C-alpha atom?
Thanks,
Suman
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blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Dear justin
I am tryinig to analyz minimum distance between periodic images, so need a new
.xtc file which has not jumps. I isse
Yes I saw your plot and it is simply around 0 with walls.
What is the field required for dielectric breakdown?
On Wed, Nov 8, 2017 at 12:18 PM, Alex wrote:
> Hi Dan,
>
> Yup, periodic, continuous, and electrically neutral. I suggested a similar
> thought in my question, i.e. with walls any tran
Hi Dan,
Yup, periodic, continuous, and electrically neutral. I suggested a
similar thought in my question, i.e. with walls any transport would
definitely be transient and self-limited. However, nothing is
transported even in the perturbative sense, as you can see from the
flux. The behavior i
On 11/8/17 12:02 PM, Wes Barnett wrote:
On Wed, Nov 8, 2017 at 11:11 AM, Shraddha Parate
wrote:
Dear Gromacs Users,
I was able to achieve a spherical water droplet without periodic boundary
conditions (PBC) by changing few parameters in the .mdp files as below:
However, I am facing th
On Wed, Nov 8, 2017 at 11:11 AM, Shraddha Parate
wrote:
> Dear Gromacs Users,
>
> I was able to achieve a spherical water droplet without periodic boundary
> conditions (PBC) by changing few parameters in the .mdp files as below:
>
> However, I am facing the following error:
>
> *Fatal error:
Hi Alex,
Is your system without walls periodic and continuous in all directions? I
can see a scenario where this sort of system will maintain charge
neutrality in the different reservoirs separated by the semi-porous
membrane. While cations will be transported, the charge in each reservoir
will be
Hello,
I am studying room-temperature ionic liquids in slab geometry and I am
experiencing that I cannot get rid of the interactions between periodic
images in the z-direction. Is there something wrong with what I am doing or
is this inevitable?
The reason I think this is because when I change "w
Thank you, it works great! I just had to rename the nucleic acids with the
prefix "D" (e.g. A to DA, G to DG ...).
On Fri, Nov 3, 2017 at 7:44 PM, Thomas Piggot wrote:
> The nucleic acid builder should do what you want:
>
> http://structure.usc.edu/make-na/
>
> Cheers
>
> Tom
>
>
> On 03/11/17 1
Dear Gromacs Users,
I was able to achieve a spherical water droplet without periodic boundary
conditions (PBC) by changing few parameters in the .mdp files as below:
*minim.mdp:*
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what t
IIRC the pdb format only allows 1 character (2 with sign) for the
charge, so you can only use integer charges. Which is pretty useless in
a MD context. So note that if you write a "pdb" with partial charges,
you're not writing pdb anymore, and I doubt anything other than
handcrafted programs will b
Hi,
I thought so because of what you said about PDB file. Yes, I will be of
course able to do it with Python.
Best wishes,
Dawid
2017-11-08 12:04 GMT+01:00 João Henriques :
> Hi,
>
> The PDB format is strict by definition (
> http://www.wwpdb.org/documentation/file-format-content/format33/sect9
You may want to consider using something a little more powerful than gmx
solvate for this, such as packmol
(http://www.ime.unicamp.br/~martinez/packmol/home.shtml).
Alternatively, you could construct a layer of water in a separate file and
concatenate them together (generate the layer of water
Hi Golnaz,
Try to increase default VdW radius scaling: option -scale in gmx solvate.
If there are large cavities in ICE you may have problem at water
interface though.
Best regards,
Alexandr
On 08/11/2017 15:04, G R wrote:
Hi All,
I’m simulating a box of tip4p ice. when I use the gmx
Hi All,
I’m simulating a box of tip4p ice. when I use the gmx solvate to fill the
top and below part of the ice surface with solvent (the solvent is tip4p
water), some of water molecules go to inside of the ice layers. I did not
receive any errors, but the coordinate files became messy after salva
Good to know, thanks.
J
On Wed, Nov 8, 2017 at 12:54 PM, Justin Lemkul wrote:
>
>
> On 11/8/17 5:52 AM, João Henriques wrote:
>
>> Hi Johannes,
>>
>> I'd suggest contacting someone at the MacKerell Lab instead. I believe
>> they
>> are responsible for the FF and for its maintenance. Otherwise t
On 11/8/17 6:25 AM, Simon Kit Sang Chu wrote:
Dear Mark,
Thank you very much. I am worried with the ends attracting each other for a
long peptide. May I ask for the general strategy simulating segments of a
protein? I believe simulating part of the whole protein might not be
something new.
Y
On 11/8/17 5:52 AM, João Henriques wrote:
Hi Johannes,
I'd suggest contacting someone at the MacKerell Lab instead. I believe they
are responsible for the FF and for its maintenance. Otherwise this issue
might get lost here and never make it to the people that absolutely need to
know about it.
On 11/8/17 5:32 AM, Hermann, Johannes wrote:
Dear all,
I do not know if this is right place to put this, please feel free to
redirect my comment.
I think I found a small typo in charmm36-jul2017 ff in the merged.rtp
file for residue NAI:
In the [ atoms ] section line
N71N HN1 0.260
Dear Mark,
Thank you very much. I am worried with the ends attracting each other for a
long peptide. May I ask for the general strategy simulating segments of a
protein? I believe simulating part of the whole protein might not be
something new.
Regards,
Simon
2017/11/8 6:37 下午 於 "Mark Abraham"
Hi,
The PDB format is strict by definition (
http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html).
Every single character (and column) within a line has a specific purpose
and charges are not included there. I doubt trjconv or other gromacs tools
will allow you to tamper wit
Dear Gromacs Users,
I have a trajectory of my MD simulation in *.gro format. Is it possible to
write the pdb snapshot
from the trajectory so that the pdb file contains the atomic charge from
top file?
The charge should be put at the end of my pdb file.
Best wishes,
Dawid Grabarek
--
Gromacs User
Hi Johannes,
I'd suggest contacting someone at the MacKerell Lab instead. I believe they
are responsible for the FF and for its maintenance. Otherwise this issue
might get lost here and never make it to the people that absolutely need to
know about it.
Look at the original paper and send an email
Hi,
AMBER didn't parameterize things that likely don't exist under biological
conditions. You can build on a proper capping group that is present in
aminoacids.trp, however, such as ACE.
Mark
On Wed, Nov 8, 2017 at 7:24 AM Simon Kit Sang Chu
wrote:
> Hi everyone,
>
> I am considering selecting
Dear all,
I do not know if this is right place to put this, please feel free to
redirect my comment.
I think I found a small typo in charmm36-jul2017 ff in the merged.rtp
file for residue NAI:
In the [ atoms ] section line
N71N HN1 0.260 69
should read
H71N HN1 0.260 69
and co
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