Dear Justin,
I've tried what you have suggested. I have used the pull code and gave 4
amino acid residues as a reference group. The location of the groups are one
below the ligand (in the protein core) and 3 were on the above ( towards the
active site gorge). When i used the code
pull
Hello All,
I am working on DNA simulations using GROMACS
Question: I created A.gro file that has DNA molecule and water molecules
within a box using GROMACS. I want to create a cylinder around the DNA so
that I can place some ions, or, compute axis of DNA so that I can place ions
closely to it
Dear Peter,
I appreciate your explanation :)
Regards,
Shima
- Original Message -
From: Peter C. Lai
To: Shima Arasteh
Cc: Discussion list for GROMACS users
Sent: Saturday, June 30, 2012 8:57 PM
Subject: Re: [gmx-users] Berger lipid
323 is proper for a higher melting point lipid
323 is proper for a higher melting point lipid like DPPC. You can easily
simulate POPC at 300, and many other people have done so. In fact I received
criticism from a reviewer as to why I picked an elevated temperature of 310,
despite the fact that 310 is physiological temperature (to make some
Hi dear gmx friends,
I have a C atom which its neighbors are N, O, H atoms and then sp2
hybridization. I wanna add this atom to the CHARMM36, but I don't know its atom
type. I checked the atomtypes.atp file in CHARMM36 package, the C types are as
below:
C 12.01100 ; carbonyl C, peptide
Yes, you are right. You wrote the tutorial for DPPC and I know that.
ok, I saw the temperatures upper than 271 K is proper for POPC. It's acceptable
that 310 mentioned in Peter's paper is correct. But I'm wondering how they
chose "310" K? In his article, he explains that their study was done i
On 6/30/12 11:03 AM, Shima Arasteh wrote:
Thanks Justin.
Yes, you are right. You wrote the tutorial for DPPC and I know that.
ok, I saw the temperatures upper than 271 K is proper for POPC. It's acceptable that 310
mentioned in Peter's paper is correct. But I'm wondering how they chose "310"
Thanks Justin.
Yes, you are right. You wrote the tutorial for DPPC and I know that.
ok, I saw the temperatures upper than 271 K is proper for POPC. It's acceptable
that 310 mentioned in Peter's paper is correct. But I'm wondering how they
chose "310" K? In his article, he explains that their stu
On 6/30/12 10:33 AM, Shima Arasteh wrote:
Dear Peter, Thanks for your link and the article. I'd like to know more about
your paper. You've mentioned in it that the temperature of POPC equilibrated,
is 310 K. As I saw in Justin's tutorial , 323 K is proper, however it was a
I'll let Peter addr
Dear Peter,
Thanks for your link and the article.
I'd like to know more about your paper. You've mentioned in it that the
temperature of POPC equilibrated, is 310 K. As I saw in Justin's tutorial , 323
K is proper, however it was a different system simulated and also many
parameters are not the
On 29/06/12 19:59, Justin A. Lemkul wrote:
Wouldn't it be nice to create a table of "standard settings" for each
forcefield
in the gmx documentation (with lit references of course)?
Well, anyone is welcome to submit anything they feel would be useful... ;)
I have considered this in the past,
Hi dear gmx friends,
I have a C atom which its neighbors are N, O, H atoms and then sp2
hybridization. I wanna add this atom to the CHARMM36, but I don't know its atom
type. How can I find its type?
Thanks for your suggestions.
Sincerely,
Shima
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