[gmx-users] about my single point calculation

from the 0-step minimization seem more reasonable than those from single point calculation with "rerun". Do you know the possible reasons which could result in the huge difference? Or I made some mistake? Thanks very much! All the best, Qinghua On Wed, Nov 6, 2013 at 4:07 P

[gmx-users] Re: single point calculation with gromacs

Dear Justin, I am sorry for the late reply. I still can't figure it out. Could you please send me the mdp file which was used for your single point calculations. I want to do some comparison and then solve the problem. Thanks very much! All the best, Qinghua -- View this message in context:

[gmx-users] Re: single point calculation with gromacs

Dear Justin, *Thanks very much for your reply! Here is my minim.mdp I used:* /; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol

[gmx-users] Re: single point calculation with gromacs

Dear Justin, *Thanks very much for your reply! Here is my minim.mdp I used:* /; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol

[gmx-users] single point calculation with gromacs

Dear All, I want to do the single point calculations for my systems with gromacs, I used the method mentioned on the gmx's website. mdrun -s sp.tpr -rerun configuration.pdb. However, I have some questions on how to generate the tpr file for single point calculation. It didn't work if I used a md

[gmx-users] Re: Energies in MM scanning using gmx

Thank you, all! I know the reason now! All the best, qh -- View this message in context: http://gromacs.5086.x6.nabble.com/Energies-in-MM-scanning-using-gmx-tp5010274p5010278.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@grom

[gmx-users] Energies in MM scanning using gmx

Dear all, But I have questions about the energies calculated by GMX for bonds and angles scanning. For example, a series of conformations of one system should be generated for a bond scanning, the only difference in geometry of these conformations is the bond length A---B. However, when I set the

[gmx-users] Charges for calculation of Coulomb interaction

Dear GMX users, Just a simple question, are the Coulomb interactions calculated using charges from ffnonbonded.itp or aminoacid.rtp? Normally, they are the same. However, if I modify some charges for some atoms (for example CB) of some residues in the aminoacid.rtp, but do not modify in ffno

Re: [gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L

Dear Dr. Vitaly Chaban, Thanks very much for your explanation. I will try to use the method as you suggested to do the validation. Thanks! All the best, Qinghua Liao On 04/09/2013 12:10 PM, Dr. Vitaly Chaban wrote: On Tue, Apr 9, 2013 at 11:03 AM, fantasticqhl <mailto:fantas

Re: [gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L

suggestions on this problems! All the best, Qinghua Liao On 04/09/2013 10:03 AM, Dr. Vitaly Chaban wrote: On Tue, Apr 9, 2013 at 9:39 AM, fantasticqhl <mailto:fantastic...@gmail.com>> wrote: Dear Dr. Vitaly Chaban, Thanks very much for your patient and detailed suggestion

Re: [gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L

. Vitaly Chaban wrote: On Mon, Apr 8, 2013 at 3:36 PM, fantasticqhl <mailto:fantastic...@gmail.com>> wrote: Dear Dr. Vitaly Chaban, Thanks very much for your patient explanation. Yeah, you are right, that is what I want to know: how you tuned this parameter? Since then,

Re: [gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L

necessary potentials (Coulombic attraction in case of OPLS). Dr. Vitaly Chaban On Mon, Apr 8, 2013 at 3:14 PM, fantasticqhl <mailto:fantastic...@gmail.com>> wrote: Dear Dr. Vitaly Chaban, Thanks very much for concern on my research! We are going to the use the bonded

Re: [gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L

ulate copper-ligand interactions using Coulomb+LJ potential only? I would guess it is a chemical bonding case. Maybe the Morse potential (additionally) can be of better service? Dr. Vitaly Chaban On Mon, Apr 8, 2013 at 1:09 PM, fantasticqhl <mailto:fantastic...@gmail.com>> wrote:

Re: [gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L

13 at 10:36 AM, fantasticqhl <mailto:fantastic...@gmail.com>> wrote: Dear Dr. Vitaly Chaban, Thanks very much for your reply. My question is the relationship between van der Waals radius and sigma in the OPLS-AA/L force filed files of Gromacs. Of course I did ab initio

Re: [gmx-users] Re: How to set the sigma and epsilon for Cu2+ in OPLS-AA/L

Dear Dr. Vitaly Chaban, Thanks very much for your reply. My question is the relationship between van der Waals radius and sigma in the OPLS-AA/L force filed files of Gromacs. Of course I did ab initio optimizations of my system, but I do not know there is some relation between the optimal bo

[gmx-users] How to set the sigma and epsilon for Cu2+ in OPLS-AA/L force field

Dear GMX users, There is a copper ion with four ligands in my system. I am going to study this system using MD simulations. For the vdW parameters, R*=1.74 angstrom and epsilon=1.14 kcal.mol from one paper will be used in our simulations. I already found the parameters of copper ion (Cu2+) in t

[gmx-users] How to modify the vdw radii of some atom?

Hi all, I want to modify the vdw radii of some atoms, but I did not find the file that I can edit for this purpose. I checked the file vdwradii.dat, but I did not find the atoms that I want to modify. Could someone tell me where I can modify them? Thanks very much! All the best, -- View thi