As suggested by you I tried using the g_angle. But got tucked. It asks for a .ndx file. I tried making it using mk_angndx but gave me an error when i used the option -type phi-psi. Although it worked well when I used the option dihedral instead of phi-psi. The .ndx file has strange nomenclature whi
You are right .. I have used g_rama for the phi-psi values. I will try g_angle as well. With -ve i meant negative values for the phi angle. As far as I understand negative phi values are sterically not allowed. let me check with the g_angle as well. Thanks for the answer as well the reference. bes
would be nice. Best regardsNavBegin forwarded message: *From: *Navratna Vajpai <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>*Date: *September 13, 2006 10:32:21 AM GMT+02:00*To: *Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>*Subject: **[gmx-users] Hi...**Reply-To
Hi all.. I wrote this mail yesterday. But could not receive any reply till now. So if someone can suggest something about it. That would be nice. Best regardsNavBegin forwarded message:From: Navratna Vajpai <[EMAIL PROTECTED]>Date: September 13, 2006 10:32:21 AM GMT+02:00To: Discussion li
Dear Eric.. Hi.. This is in regard to your previously replied mail regarding the use of GROMOS96 or OPLS-AA or AMBER force field.As you said it depends upon the users taste which one to use. This means that the three on a broad manner should give convergence of the analyzed data set. Infact from my
Dear All..to continue the run, as i understood, I modified the md.mdp and then use the .tpr and .trr for the further run. Can anyone suggest that it is the right way or not? actually in one of the tutorials note i have just found to change the options as -time $value -until $value. I was wondering
HN. Now I exactly don't know which type of atoms are defined there. Kindly let me know what should I do to bring HA into the scene. use an all atom force field. Best regardsNavOn Aug 17, 2006, at 5:46 AM, Mark Abraham wrote: Navratna Vajpai wrote: Dear All I have been able to carry on with t
Dear MarkHello.The force field I used is g43b1 from GROMOS96. I checked the g43b1.atp file and fond that the HC is defined there which corresponds to Hydrogen attached to the Carbon. But somehow in the pdb outcome this is not there. the output pdb file contains only H atoms corresponding to HN. Now
Dear All I have been able to carry on with the MD run of my peptides. But when I converted the traj into the pdb file I realized that there are no HA atoms in the pdb. I checked the rtp file and found that even those atoms are not defined there. So can anyone tell me how to get the HA (after or bef
Many thanks Eric, it worked. I didn't really had look into this.Best regardsNavOn Aug 16, 2006, at 11:34 AM, Erik Marklund wrote:On Wed, 2006-08-16 at 10:07 +0200, David van der Spoel wrote: Navratna Vajpai wrote: Hey Mark..I had attached the file along with the mail. I think you could not re
Hey Mark..I had attached the file along with the mail. I think you could not receive it. let me paste the contents and explain it little more. I am trying to run the simulation in vacuum of a nona peptide. I managed to get pdb2gmx working and even further the EM working. But when I tried to do the
Dear All... I was trying to move further and finally managed to move forward. I am explaining the problem in little more detail. The problem arises when the grompp before the mdrun is executed. I don't know why but it ask for -n option for its execution. I tried that also but still the error stays.
Dear All .. I have only recently started the GROMACS package. I want to run a MD simulation in vacuum for 5 ns say. I have tried to edit the demo file which comes with the GROMACS package. but Some how it give an error. Which I am still unable to solve. I am atttaching the file under this. Could an
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