Well, none of us in this project have the scripting skills necessary for this, that's sort of the problem...
Thanks,
Alex
Hi Alex,
I think the best way is to extend the chain, such that you get an overlap between both ends. So for a stretch of DNA
ACGT
You would generate
TACGTA
Then
Dear All,
In the on-line lysozyme tutorial, it gives a series of mdp files. But it
meantioned for different force fields the options should be different.
Will you please tell me regardless of force fields, whether all the
cutoff-scheme can be Verlet? Besides I can change the rcoulomb and
Hi,
Files in fixed-column formats use the column widths to separate elements.
They don't use white space at the same time, for the same job! Try it and
see ;-)
Mark
On 26/04/2015 6:29 am, Brett brettliu...@163.com wrote:
Dear All，
If we change HIS188 in Chain B to HISE188 in Chain B, before
Hi Alex,
I think the best way is to extend the chain, such that you get an overlap
between both ends. So for a stretch of DNA
ACGT
You would generate
TACGTA
Then you strip off the terminal atoms and rewire the links over the
boundary. It requires renumbering the topology and at first looks a
Hi,
Look at the whole molecule topology. Don't ignore any warnings.
Mark
On 26/04/2015 9:38 am, Eric Smoll ericsm...@gmail.com wrote:
Hello Gromacs Users,
I have constructed a multi-component solution and, during energy
minimization, one molecule type is radically deforming under ~ 0.2 ps.
Hello Gromacs Users,
I have constructed a multi-component solution and, during energy
minimization, one molecule type is radically deforming under ~ 0.2 ps. All
molecules of this type explode simultaneously. Looking over the topology,
all the atoms in this molecules appear to have correct
Dear All,
For the grpmacs analysis purpose, from the official GRACE site I have
downloaded and installed different versions of GRACE, some was said to
definitely contains xmgrace. But after installation, none contains xmgrace,
they contain grace or gr in the bin folder. After I invoke the
The issue is, no mater grace or xmggrace I download, I cannot have the xmgrace
exe file in the corresponding bin folder produced.
Thus will you tell me which version of grace has the xmgrace after unpack and
installation?
Brett
At 2015-04-26 23:09:23, abhijit Kayal
On 4/26/15 8:54 AM, fatemeh ramezani wrote:
Dear gmx-usersI want to calculate free energy of binding of ligand to Au
surface in 8 ns simulation. I considered 7 lambda (lambda= 0, 0.2, 0.4, 0.6,
0.8, 0.9, 1) and for every lambda a mdp file. for example lambda-0 mdp file:
title =
Hi Agnivo,
Temperature gradient means non-equilibrium MD (NEMD)
See notes from Prof. Martini:
https://nanohub.org/resources/7582/download/Martini_L10_NonequilibruimMD.pdf
What observable would you like to measure? Lets say you want to
measure observable A.
One procedure I can think of:
1.
Dear Tsjerk,
Will you please explain to me why the RMSD in this step is so large? For this
reason I think there is something wrong.
I am looking forward to getting a reply from you.
Brett
At 2015-04-26 20:59:59, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Brett,
Too high for what?
the command is xmgrace, try with xmgrace -nxy.
On Sun, Apr 26, 2015 at 7:01 AM, Brett brettliu...@163.com wrote:
Dear All,
For the grpmacs analysis purpose, from the official GRACE site I have
downloaded and installed different versions of GRACE, some was said to
definitely contains
On 4/26/15 9:53 AM, Brett wrote:
Dear Tsjerk,
Will you please explain to me why the RMSD in this step is so large? For this
reason I think there is something wrong.
No, there's nothing wrong; the analysis in this case is meaningless.
Energy minimization inherently makes large (orders of
Hi Brett,
Too high for what?
You do EM because you just built (part of) your system, and in doing so
introduced clashes and non-ideal geometries. These lead to high potential
energy, so you relax them with EM. What you see is how much the system
relaxed. Noone usually cares how much potential
Dear All,
I just run the command gmx energy -f em.edr -o potential.xvg for my energy
minimization step MD, but I find the RMSD given by this command is 142611,
which I regard to be too high.
Will you please explain to me what leads to the so high RMSD (Err.Est is 53000,
Tot-Drift is -341107
Dear gmx-usersI want to calculate free energy of binding of ligand to Au
surface in 8 ns simulation. I considered 7 lambda (lambda= 0, 0.2, 0.4, 0.6,
0.8, 0.9, 1) and for every lambda a mdp file. for example lambda-0 mdp file:
title = n.pdb restraining
cpp =
Hi Agnivo;
Yes, the idea of freezing the solvent or the protein in many times is
to sample the non-equilibrium thermal process. It will remain in the
target temperature on average, over many fixed configurations obtained
by different NVT runs (equilibrium runs). But you may need to run this
many
Hello Users,
This is in relation to my previous posts.
I am looking to replicate the figure below :
tempgradient.png
https://docs.google.com/file/d/0B-U8uULVZjfRQWlHeHVJdDJjcms/edit?usp=drive_web
Basically I am following this paper for my work :
Lervik_ProtWatInterHT_2009.pdf
On 4/26/15 7:42 PM, Brett wrote:
Dear Justin,
I mean why the RMSD is such huge. Does it mean in the energy mminimization step
the protein has moved from point A to point B which is long long distance away
from point A but, although the protein has been continously embedded in water?
If the
Hello all,
Thanks to Dr. Lemkul for asking.
This is what I did to reach my present state :
(a) Prepared the topology of the system using GROMOS96 43a2 ff and energy
minimized the system after solvation using steepest descent algorithm.
(b) Did a position restrained ( protein ) 5 ns
Fatal
Hello all,
Thanks to Dr. Lemkul for asking.
This is what I did to reach my present state :
(a) Prepared the topology of the system using GROMOS96 43a2 ff and energy
minimized the system after solvation using steepest descent algorithm.
(b) Did a position restrained ( protein restrained ) 5 ns
Dear Justin,
I mean why the RMSD is such huge. Does it mean in the energy mminimization step
the protein has moved from point A to point B which is long long distance away
from point A but, although the protein has been continously embedded in water?
If the RMSD is above several thousands, it
On 4/26/15 7:07 PM, Agnivo Gosai wrote:
Hello Users,
This is in relation to my previous posts.
I am looking to replicate the figure below :
tempgradient.png
https://docs.google.com/file/d/0B-U8uULVZjfRQWlHeHVJdDJjcms/edit?usp=drive_web
Basically I am following this paper for my work :
On 4/26/15 8:14 PM, Agnivo Gosai wrote:
Hello all,
Thanks to Dr. Lemkul for asking.
This is what I did to reach my present state :
(a) Prepared the topology of the system using GROMOS96 43a2 ff and energy
minimized the system after solvation using steepest descent algorithm.
(b) Did a
Hello,
I am copy pasting my mdp file for the last step of my procedure :
Here I am not using any freeze group.
; Run parameters
integrator = md; leap-frog integrator
nsteps = 5; 100 ps
dt = 0.002 ; 2 fs
energygrps = Protein
Dr. Lemkul
Thanks for such an easy fix to my problem. I guess I have been doing all
sort of weird stuff since last night instead of thinking logically and
reading the relevant portion of the manual.
Thanks Regards
Agnivo Gosai
Grad Student, Iowa State University.
--
Gromacs Users mailing list
Hello users,
Thanks a lot Suzen for an insightful suggestion. My protein and solvent
have been equilibrated at 300 K in an NVT ensemble.
I raised the temperature of protein gradually by using simulated annealing
to 400 K and the solvent has been kept at 300 K.
Now I wish to get a temperature
On 4/26/15 3:40 PM, Eric Smoll wrote:
Hello Dr Lemkul,
Thank you for the clarification. To summarize: If I have a bond between two
atoms and one of the atoms has a topology atom field that begins with the
letter H, constraints=h-bonds will transform it into a constraint.
Exactly.
I have
Hello Dr Lemkul,
Thank you for the clarification. To summarize: If I have a bond between two
atoms and one of the atoms has a topology atom field that begins with the
letter H, constraints=h-bonds will transform it into a constraint.
I have another question. When specifying this constrained
Dear Gromacs Users,
I would appreciate you to give me any comments or hints about the question
below.
What makes the calculation time much longer when I calculate a solvation free
energy using the mdp input1 compared to the mdp input2?
Input1
Free_energy = yes
Couple-lambda0=
Dear All,
In the on-line Justin tutorial on lysozyme, the several mdp files are for the
specific force field OPLS-AA force field. It specifically mentioned Settings,
particularly nonbonded interaction settings, will be different for other force
fields.
Will you please introduce to me how to
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