Just to be complete: I am using following command to populate system with
SPC water using genbox:
genbox -cp slab_wligf.gro -cs spc216.gro -vdwd 0.5 -box 3.081 3.637 11.07514
Thanks
Chetan
On Wed, Jun 25, 2014 at 7:48 PM, Chetan Mahajan
wrote:
> Dear All,
>
> I have a system of a crystal slab
Dear All,
I have a system of a crystal slab at the center of the box surrounded by
water. I am using position restraints for crystal. I am observing a weird
thing that after NPT equilibration of system populated with SPC water using
gromacs genbox command, some kinda hole or vacuum appears in the
Thanks, Mark. I was translating a crystal and for some reason, C atom of
formate was getting displaced. Now, it's working.
On Wed, Jun 25, 2014 at 7:16 AM, Mark Abraham
wrote:
> Why do you have a bonded interaction whose length is 1.6nm? Mdrun is
> telling you that is limiting you.
>
> Mark
> O
On 6/25/14, 4:04 PM, Zheng Ruan wrote:
Hi,
I'm new to gromacs and right now I'm trying to use g_hbond to analyze
my trajectory. Basically, I create two selections in .ndx file and try
to find hydrogen bonds between them. In the output, there is a
"y-axis" record in hbond.xpm matrix file. The n
On 6/25/14, 11:55 AM, Michael Weiner wrote:
Hello, I've built a lipid bilayer in Martini consisting of DPPC, DUPC, and
cholesterol. When I try to do an energy minimization using the
minimization.mdp provided in the Martini lipid bilayer tutorial
(http://md.chem.rug.nl/cgmartini/index.php/bilay
On 6/25/14, 10:12 AM, Iris Nira Smith wrote:
Hello gromacs users,
I have searched the gmx-users archive and have successfully found multiple
posts that provide advice on how to troubleshoot my issue. Unfortunately, after
trying multiple ways to troubleshoot as suggested by each of these post
Hi,
I'm new to gromacs and right now I'm trying to use g_hbond to analyze
my trajectory. Basically, I create two selections in .ndx file and try
to find hydrogen bonds between them. In the output, there is a
"y-axis" record in hbond.xpm matrix file. The number of the elements
of "y-axis" is the sa
Hi all,
I'm having trouble replicating the VDW energy from a shifted potential.
When I calculate unshifted potentials by hand, I get an answer that agrees
with GROMACS. When I calculate shifted potentials, I don't. I've included
the intermediate numbers I get as well as a simple GROMACS test case,
PS: [Perhaps stating the obvious] Using an overly aggressive
Hamiltonian scaling will only result in bad mixing at high
temperatures and therefore low efficiency, hence wasted compute time,
but it should not "hurt" your results. It is still quite useful to
ensure that you're not sampling an entire
Hi,
Next time, you should perhaps use "plz, ..." (and other eye-catching
formatting marks); a nice mix of font colors and typefaces could also
help to highlight your questions. :D
On Tue, Jun 24, 2014 at 10:32 PM, Thomas Evangelidis wrote:
> Greetings,
>
> I want to use the HREX implementation o
Hello,
I've built a lipid bilayer in Martini consisting of DPPC, DUPC, and
cholesterol. When I try to do an energy minimization using the
minimization.mdp provided in the Martini lipid bilayer tutorial
(http://md.chem.rug.nl/cgmartini/index.php/bilayers), I get a large number
(several dozen) o
Hello gromacs users,
I have searched the gmx-users archive and have successfully found multiple
posts that provide advice on how to troubleshoot my issue. Unfortunately, after
trying multiple ways to troubleshoot as suggested by each of these posts, I am
still having the same issue.
I successf
Hello,
i'm interested in change of free energy of protein + ligand complex upon
mutation. While there's some information and tutorials on decoupling of
small molecules in water, i found little information on set up for free
energy upon mutation, with a dated toluene -> p-cresol tutorial by
Gi
On Jun 25, 2014 8:15 AM, "suhani nagpal" wrote:
>
> Greetings
>
> I have been trying to run a few set of simulations using high number of
> processors.
>
> Using the tutorial -
>
http://compchemmpi.wikispaces.com/file/view/Domaindecomposition_KKirchner_27Apr2012.pdf
>
> I have done calculations to
Why do you have a bonded interaction whose length is 1.6nm? Mdrun is
telling you that is limiting you.
Mark
On Jun 25, 2014 12:26 PM, "Chetan Mahajan" wrote:
> Hello,
>
> I have 10910 atoms ( 2160 of TiO2, 5 of sodium and formate, rest water) in
> my system. I am getting following error:
>
>
> F
Thanks Justin...I will check for this.
Regards
Lovika
On Wed, Jun 25, 2014 at 5:31 PM, Justin Lemkul wrote:
>
>
> On 6/25/14, 8:00 AM, Lovika Moudgil wrote:
>
>> Hi Everyone...Need some help...
>>
>> I got the following error in my mdrun Plese help me to understand this
>> error...What th
On 6/25/14, 8:00 AM, Lovika Moudgil wrote:
Hi Everyone...Need some help...
I got the following error in my mdrun Plese help me to understand this
error...What this error is all about and what should I do to remove this .
---
Program mdru
Hi Everyone...Need some help...
I got the following error in my mdrun Plese help me to understand this
error...What this error is all about and what should I do to remove this .
---
Program mdrun, VERSION 4.6.5
Source code file:
/home/itlab/
On 6/25/14, 6:25 AM, Chetan Mahajan wrote:
Hello,
I have 10910 atoms ( 2160 of TiO2, 5 of sodium and formate, rest water) in
my system. I am getting following error:
Fatal error:
There is no domain decomposition for 16 nodes that is compatible with the
given box and a minimum cell size of 1.
Hello,
I have 10910 atoms ( 2160 of TiO2, 5 of sodium and formate, rest water) in
my system. I am getting following error:
Fatal error:
There is no domain decomposition for 16 nodes that is compatible with the
given box and a minimum cell size of 1.81239 nm
Change the number of nodes or mdrun op
On 6/25/14, 4:44 AM, mirko busato wrote:
Thank you very much,
In my analysis ,I would like to consider Hydrogen bonds involving S atom as
well. I think that g_hbond is not built to manage Hydrogen bonds with S.
Do you know if there are available scripts? or Could you suggest me something
t
On 6/25/14, 4:42 AM, Dawid das wrote:
Dear Gromacs experts,
I have a few questions regarding adding a new residue to the force field.
1) In what unit should provide force constants for stretching, bending and
torsion in aminoacids.rtp file? I can't really figure that out from gromacs
manual.
On 6/25/14, 12:52 AM, Andy Chao wrote:
Hi,
I have a few technical questions regarding creating the topology file by
using the command "g_x2top".
I would like to use the following GROMACS's command:
g_x2top -f device.gro -ff oplsaa -o device.top
to convert the .gro file to .top.
The problem
On 6/24/14, 11:07 PM, sunyeping wrote:
Dear all,In my NPT explicit solvent simulation on the proteins with multiple
chains, sometimes the protein can break up and its chains leave far from each
other. We wonder if this is caused by the instability of the protein or
improper simulation condit
On 6/24/14, 2:11 PM, ram bio wrote:
shall i do only two tc-grps protein and non-protein?
Not for a membrane protein system, no. I'd say your complex, the lipids, and
solvent+ions in three groups is the most common approach.
-Justin
On Tue, Jun 24, 2014 at 12:18 PM, Justin Lemkul wrot
Thank you very much,
In my analysis ,I would like to consider Hydrogen bonds involving S atom as
well. I think that g_hbond is not built to manage Hydrogen bonds with S.
Do you know if there are available scripts? or Could you suggest me something
to solve this problem?
I really appreciate yo
Dear Gromacs experts,
I have a few questions regarding adding a new residue to the force field.
1) In what unit should provide force constants for stretching, bending and
torsion in aminoacids.rtp file? I can't really figure that out from gromacs
manual.
2) If I provide those constants and natur
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