In God We Trust
Hello Dear gmx-users
I want to simulate oliver oil by Gromacs. I made topology of triolein with
G45a3 force field at NPT ensemble (according to SCHULER paper ; Journal of
Computational Chemistry, Vol. 22, No. 11, 1205–1218 (2001).I
generated a box with 216
On 7/06/2012 4:33 AM, ramesh cheerla wrote:
Dear Mark,
Thank you for your reply, According to my
understanding functional form of dihedral function type 9 is same as
dihedral function type 1 i.e k (1 + cos(n (phi)- phi s)) except
the difference that function type 9
Did you play with the time step? Just currious, but I woundered what happened
with 0.0008, 0.0005, 0.0002. I found if I had a good behaving protein, as soon
as I added a small (non-protein) molecule which rotated wildly while attached
to the protein, it would crash unless I reduced the time
Dear Mark,
I am very Thankful to you for your valuable suggestion.
On Thu, Jun 7, 2012 at 12:04 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 7/06/2012 4:33 AM, ramesh cheerla wrote:
Dear Mark,
Thank you for your reply, According to my
understanding
Dear Gromacs Users,
I am using gromacs version 4.5.5.and running my jobs on single node with 8
cores. My system contains about 425000 atoms (protein + Lipid +SOL). I have
successfully reached up to Energy minimization step.As per the suggestion
by Dear Mark, I am starting my NPT equilibration
On 7/06/2012 8:33 PM, PAVAN PAYGHAN wrote:
Dear Gromacs Users,
I am using gromacs version 4.5.5.and running my jobs on single
node with 8 cores. My system contains about 425000 atoms (protein +
Lipid +SOL). I have successfully reached up to Energy minimization
step.As per the suggestion
On 6/7/12 3:57 AM, lloyd riggs wrote:
Did you play with the time step? Just currious, but I woundered what
happened with 0.0008, 0.0005, 0.0002. I found if I had a good behaving
protein, as soon as I added a small (non-protein) molecule which rotated
wildly while attached to the protein, it
On 6/6/12 1:12 PM, Sangita Kachhap wrote:
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On 6/7/12 2:55 AM, bipin singh wrote:
Hello All,
I have a doubt regarding -tsham option of g_sham (single histogram analysis).
While using g_sham do we need to mention the temperature at which simulation
were performed or it should be the constant (298.15K) for all analysis ( no
matter at
Dear gmxers,
I am performing COM pulling using GMX4.0.7, to obtain the PMF as a function of
distance between the COMs of two molecules. However, quite strange resuluts are
generated, i.e., the distance can not be fixed at the value defined by
pull_init1. The pull opinions are given below.
On 6/7/12 7:38 AM, xiaowu759 wrote:
Dear gmxers,
I am performing COM pulling using GMX4.0.7, to obtain the PMF as a function of
distance between the COMs of two molecules. However, quite strange resuluts are
generated, i.e., the distance can not be fixed at the value defined by
pull_init1. The
Dear Justin,
Greetings of the day!!
I am following your tutorial for the calculation of free energy change in
gromacs.
It says about the change in state A and state B. I have a query regarding
these states. What are the 2 states A and B in the tutorial and how can I
define these 2 states for my
?
That's your judgement to make. How does your preparation protocol
compare to the ones you have read about in the recent literature?
Mark
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On 6/7/12 8:26 AM, neeru sharma wrote:
Dear Justin,
Greetings of the day!!
I am following your tutorial for the calculation of free energy change in
gromacs.
It says about the change in state A and state B. I have a query regarding these
states. What are the 2 states A and B in the
Date: Thu, 07 Jun 2012 07:59:27 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] How to set up constraint distcance pulling
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4fd0979f.4020...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1;
On 6/7/12 9:14 AM, xiaowu759 wrote:
Date: Thu, 07 Jun 2012 07:59:27 -0400
From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
Subject: Re: [gmx-users] How to set up constraint distcance pulling
To: Discussion list for GROMACS users gmx-users@gromacs.org
mailto:gmx-users@gromacs.org
Hi all,
I downloaded the original form of DSSP which is recently called
DSSPold. Whenever I use the following:
*do_dssp -s topol.tpr -f t raj.xtc -o ss.xpm *
It selects Protein by it-self without any control from me. I want to
choose from the list, for example not protein but C-alpha.
To
On 6/7/12 10:07 AM, Turgay Cakmak wrote:
Hi all,
I downloaded the original form of DSSP which is recently called
DSSPold. Whenever I use the following:
*do_dssp -s topol.tpr -f t raj.xtc -o ss.xpm *
It selects Protein by it-self without any control from me. I want to choose
from the
Message: 1
Date: Thu, 07 Jun 2012 08:53:22 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] Regarding Free Energy calculation tutorial
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4fd0a442.6000...@vt.edu
Content-Type: text/plain;
Hi Justin,
Thank you for your descriptive reply.
I prepared new index.file which includes mainchain, and when I used the
do_dssp with -n index.ndx, it worked.
But, if I doesn't use the index file, again, the Protein is selected by
the system. It is weird..
Best regards,
Deniz
On Thu, Jun 7,
Dear justin Thank you for your previous Valuable reply.
To do
umbrella sampling should i run more number of steps than i run in Umbrella
pulling ?
otherwise if i use lesser number of steps in Umbrella sampling than
On 6/7/12 12:26 PM, vidhya sankar wrote:
Dear justin Thank you for your previous Valuable reply.
To do umbrella sampling should i run more number of steps than i run in Umbrella
pulling ?
That depends on how many steps were used for the pulling. Also note that the
pulling step represents
Any suggestions on this topic?
Thanks again for your time.
Dear Gromacs Users,
I am trying to find out the relative free energy difference of binding of
a ligand with wild type protein (Glutamate residue) and mutant protein
(Alanine residue).
For charge part of the mutation, this is what
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Wednesday, June 6, 2012 4:08 PM
Subject: Re: [gmx-users] Atomtype OW_tip4p not found
On 6/6/12 7:36 AM, Amir Abbasi wrote:
On 6/7/12 6:18 PM, Amir Abbasi wrote:
*From:* Justin A. Lemkul jalem...@vt.edu
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Wednesday, June 6, 2012 4:08 PM
*Subject:* Re: [gmx-users]
On 6/7/12 7:28 PM, Edward Deira wrote:
Dear all,
I'm currently starting to dwell deeper in MD, and I'm taking some time to
understand what's going on inside the gromacs black-box.
In one of those dwellings, I came across an older post
Hi,
I am working through the KALP-15 in DPPC tutorial (only using a different
protein) and having difficulties in packing the lipids around the protein.
After I scaled the lipid positions by a factor of 4 (perl inflategro.pl
system.gro 4 DPPC 14 system_inflated.gro 5 area.dat) and ran energy
On 6/7/12 7:48 PM, Erica Hicks wrote:
Hi,
I am working through the KALP-15 in DPPC tutorial (only using a different
protein) and having difficulties in packing the lipids around the protein.
After I scaled the lipid positions by a factor of 4 (perl inflategro.pl
system.gro 4 DPPC 14
Hi,
After Successfully neutralizing and sd minimization of the system, I got
the below error when I try the grompp for position restrained step. The
command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p complx.top -o
complx_eqn1.tpr
Any help will be highly appreciated.
Many thanks.
On 8/06/2012 12:23 PM, Malai wrote:
Hi,
After Successfully neutralizing and sd minimization of the system, I
got the below error when I try the grompp for position restrained
step. The command I used is :grompp -v -f eqn1.mdp -c complx_sd.pdb -p
complx.top -o complx_eqn1.tpr
Any help will
Dear Mark,
Thanks for mail. you mean I need to define in mdp file?. Can you please
guide me how to do that. Thanks.
On Fri, Jun 8, 2012 at 10:30 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 8/06/2012 12:23 PM, Malai wrote:
Hi,
After Successfully neutralizing and sd minimization of the
On 7/06/2012 10:51 PM, PAVAN PAYGHAN wrote:
Dear Mark,
Thank you very much for the reply.
To clarify , I have asked all the warning based questions to get
acknowledged with your expert opinion, apart from the manual based view.
According to your suggestion NPT with Position restraints is
On 8/06/2012 12:34 PM, Malai wrote:
Dear Mark,
Thanks for mail. you mean I need to define in mdp file?.
No. Using one of the two ways I suggested earlier depend what you're
actually trying to do, but since your intention in using the CA group is
unknown to us, you're preventing yourself
Dear MARK,
Dear Mark,
Thanks for mail. you mean I need to define in mdp file?.
No. Using one of the two ways I suggested earlier depend what you're
actually trying to do, but since your intention in using the CA group is
unknown to us, you're preventing yourself getting specific help.
Hi,
I am trying to use a table potential implementing Weeks-Chandler-Anderson
(WCA) interaction between a solute and all atoms of a solvent like TIP3P water
( with nonzero interaction in the Hydrogen atoms) . But, I am having a trouble
in specifying energy groups required for table potential.
On 8/06/2012 1:09 PM, Sanku M wrote:
Hi,
I am trying to use a table potential implementing
Weeks-Chandler-Anderson (WCA) interaction between a solute and all
atoms of a solvent like TIP3P water ( with nonzero interaction in the
Hydrogen atoms) . But, I am having a trouble in specifying
Dear all gromacs users,
While running the grompp commond after
addition of counter ions i am getting the following error.
Fatal error:
number of coordinates
in coordinate
Have you incorrectly changed the numbers in the topology, the difference in the
number is 8, so it appears your coordinate file contains 8 more atoms than the
topology. You will have to work out how that is.
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical
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