Thanks, and now after some time I get:"Pull reference distance for coordinate 3
() needs to be non-negative"How to solve this error?
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Is the modified parameter file for POPG from your work available online?
Merril.
On 10 Mar 2017 7:05 a.m., "Merril Mathew" wrote:
> many thanks Tom.
>
> On 10 Mar 2017 1:35 a.m., "Thomas Piggot" wrote:
>
>> So this isn't a berger based PG rather a pure GROMOS one. But yes, it
>> also has probl
many thanks Tom.
On 10 Mar 2017 1:35 a.m., "Thomas Piggot" wrote:
> So this isn't a berger based PG rather a pure GROMOS one. But yes, it also
> has problems. The double bond dihedrals don't work well and so you get
> really poor order parameters after the double bond (see
> http://pubs.acs.org/
Dear all,
I have two systems: 1. metal ion in water with a counter ion present in the
bulk & 2. Exactly same system (with same no. of atoms as the previous one) with
counter ion present in metal's first solvation shell.
Will it be fair to compare the total energies of both the systems obtaine
So this isn't a berger based PG rather a pure GROMOS one. But yes, it
also has problems. The double bond dihedrals don't work well and so you
get really poor order parameters after the double bond (see
http://pubs.acs.org/doi/abs/10.1021/ct3003157 for POPC but the same is
true of POPG). From wh
thanks Justin.
On 8 Mar 2017 13:09, "Justin Lemkul" wrote:
>
>
> On 3/8/17 8:06 AM, Merril Mathew wrote:
>
>> I dont know what I am doing wrong. There is no Box-X or Box-Y when
>> prompted. These are the list I get:
>> -
>> 1 Ang
On 3/9/17 2:41 PM, Wally Davis wrote:
My input line is:
gmx order -s test.tpr -f fullTraj.trr -n orderParam.ndx
The index file is formated with 3 groups, one per carbon along the chain of
interest.
The error I get is: "In option nr Required option was not provided, and the default
file 'inde
I also used the same POPG .itp and .pdb files to edit and create an
oxidised version of the molecule with aldehyde group replacing the double
bond. Is there a problem associated with parameters from A Kukol for POPG?
On 10 Mar 2017 00:45, "Merril Mathew" wrote:
> The POPG .itp and .pdb files wer
The POPG .itp and .pdb files were obtained from,
https://lipidbook.bioch.ox.ac.uk/package/show/id/16.html
Author : A Kukol.
I used D-POPG. Should I use electron density or mass for calculating
monolayer thickness?
Merril.
On 10 Mar 2017 00:36, "Thomas Piggot" wrote:
> How did you get/make the
How did you get/make the itp for POPG, this isn't available from the
Tieleman group website. The Berger parameters don't work well for PG.
For example, you will see ring like structures in the head group if you
look at the simulations in something like VMD. The APL for bilayers (and
I imagine m
I am using Berger lipid from Dr.Tielemens website and modified the gromos
forcefield to include the lipid parameters. Out of interest, Do you know
any gromacs tools or other programs that calculatg the area per lipid and
bilayer thickness for monolayers? I tried to use GridMAT-MD and FATSLiM but
it
Sort of. The saturated carbons after the double bond will be correct
too, just not C9 and C10 in the double bond (as you need different
assumptions for calculating these in united-atom system which the -unsat
option is meant to do correctly but doesn't). Additionally, there are
tools out there
Hi,
I am using a united atom forcefield. gromos53a6. So does that mean as long
as I avoid the double bond and the subsequent carbons after the double
bond, then the calculation is correct? I understand it does not describe
the full lipid length but can be used to assess the monolayer behaviour
ro
The order parameters calculated for all the saturated carbons will be
correct but the gmx order program doesn't calculate the order parameters
for the unsaturated carbons correctly (even when using the -unsat option).
Out of interest, is this a united-atom or all-atom force field you are
using
Hi,
I followed turorials found on Bevanlab by Justin. I successfully calculated
order parameter for DPPC molecules in my system following the tutorial. My
question is whether the same calculation can be applied for a POPG molecule
with a double bond in the acyl chain.? can I group all the carbon u
My input line is:
gmx order -s test.tpr -f fullTraj.trr -n orderParam.ndx
The index file is formated with 3 groups, one per carbon along the chain of
interest.
The error I get is: "In option nr Required option was not provided, and the
default file 'index' does not exist or is not accessible.
Hi,
See also
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume
Mark
On Thu, Mar 9, 2017 at 5:04 PM wrote:
> Thank you for yours answers .
>
> I'm a felling more comfortable.So to sum up my index file is filled with
> the coordonate that i care.
> So in my case if
Thank you for yours answers .
I'm a felling more comfortable.So to sum up my index file is filled with the
coordonate that i care.
So in my case if i want only the RNA i just have to delete all the others
data.And when i run my .xtc for make it shorter il 'll have only water
Or i have just to c
Hi,
On Thu, Mar 9, 2017 at 3:11 PM wrote:
> Hello.
>
> I am new on using gromacs and i have problems with my files .I need to
> remove water and ions from an .xtc in order to keep my RNA.Then i have to
> center the system in the box and remove some frame to be able to visualize
> it.
>
> Here ar
Hello.
I am new on using gromacs and i have problems with my files .I need to remove
water and ions from an .xtc in order to keep my RNA.Then i have to center the
system in the box and remove some frame to be able to visualize it.
Here are the commands lines that i use:
trjconv -f gold.xtc -s
On 3/9/17 3:00 AM, Vytautas Rakeviius wrote:
Hello,
I want to drag two atoms together with GROMCS SMD options.But I tried different
options and still those groups are pushed away one from another.I would be very
thankful if someone edits this code example (from:
http://www.bevanlab.biochem.v
Dear colleagues,
We are willing to invest on nodes for GROMACS-specific calculations, and
trying to best the best for our bucks (as everyone).
For now our decisions comes close to nodes using the following
configuration:
2 * Xeon E5-2630 v4
1 P100 or 2 * P5000 or 2 * K40
Cluster node interc
Hello,
I want to drag two atoms together with GROMCS SMD options.But I tried different
options and still those groups are pushed away one from another.I would be very
thankful if someone edits this code example (from:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrell
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