[gmx-users] Re: COM Pulling

2012-06-30 Thread Raj
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

[gmx-users] DNA simulations

2012-06-30 Thread SatyaK
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

Re: [gmx-users] Berger lipid

2012-06-30 Thread Shima Arasteh
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

Re: [gmx-users] Berger lipid

2012-06-30 Thread Peter C. Lai
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

[gmx-users] atom type

2012-06-30 Thread Shima Arasteh
 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

Re: [gmx-users] Berger lipid

2012-06-30 Thread Shima Arasteh
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

Re: [gmx-users] Berger lipid

2012-06-30 Thread Justin A. Lemkul
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"

Re: [gmx-users] Berger lipid

2012-06-30 Thread Shima Arasteh
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

Re: [gmx-users] Berger lipid

2012-06-30 Thread Justin A. Lemkul
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

Re: [gmx-users] Berger lipid

2012-06-30 Thread Shima Arasteh
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

Re: [gmx-users] Structure optimization failure

2012-06-30 Thread ms
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,

[gmx-users] atom type

2012-06-30 Thread Shima Arasteh
 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 -- gmx-users mailing listgmx-users@gromac