Re: [gmx-users] H-REMD in umbrella sampling

Hi, The method I suggest is this: 1) It is possible in gromacs to do HREMD using free energy parameters in mdp and "-replex N" option in gmx mdrun. 2) It is possible to set harmonic potential length as parameter changing with lambda So, the goal is to set harmonic potential between COMs of

[gmx-users] How to monitor restrained force (F_i) used for distance restraints

Dear Gromacs users, Is there someone that can help me to monitor the restrained force (F_i in equation 4.77 of manual) used for distance restraints? Any help would be appreciated. -- Thanks & Regards, Yuno Lee, Ph.D. --- School of Computational Sciences,

Re: [gmx-users] H-REMD in umbrella sampling

On 11/24/15 12:06 PM, adam wrote: Hi, Thank you for the advice. Though, I am a bit confused how one could implement such particles in practice. What do you understand by “make two virtual particles” ? Where it should be defined in gromacs inputs ? Also, as I understand, if I run standard

Re: [gmx-users] H-REMD in umbrella sampling

Hi, Thank you for the advice. Though, I am a bit confused how one could implement such particles in practice. What do you understand by “make two virtual particles” ? Where it should be defined in gromacs inputs ? Also, as I understand, if I run standard umbrella sampling simulation with the

Re: [gmx-users] Problem with running crystal simulation

Hello, Ben, Does the system blow up during NVT simulations (pcoupl = no) with either box size? Simply increasing the box size without adjusting the system (adding more atoms if you have a periodic molecule, for example) usually makes matters worse. Can you give a more detailed description of

[gmx-users] Explicit and implicit solvent

Hi everyone, I am really confused between explicit and implicit solvent model. Any good resource will be helpful to me. I am using CHARMM forcefield and TIP4P water model. I guess it is explicit water model. Can anyone correct me? Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB

Re: [gmx-users] Explicit and implicit solvent

Let me suggest that you first start by the very basics: https://en.wikipedia.org/wiki/Implicit_solvation Google (or any other search engine) is your friend, costs nothing, and it's virtually instantaneous. GROMACS manual is also another good place to start. Also, yes TIP4P is an explicit water

Re: [gmx-users] Problem with running crystal simulation

Hi Elton, Thank you for your reply. I have increase my box size to 10 10 10. However it is still blowing up. Yes I am trying to run NPT simulation, will freezing the crystal framework will cause the box to blow up? Because I am doing an adsorption simulation hence I need the crystal stay in

[gmx-users] convert amber files to gromacs

Hi everybody,   I want to convert the topology and coordinate files fromamber to gromacs format. I used acpype bu it didn’t work properly (actually mysystem is consisted of some lipids in a water-protein system but when I convertthe files via acpype, the backbone is consisted of a mass

[gmx-users] Umbrella sampling with spherical coordinate

Hi all, To find out leaving pathway of metal ion from metal binding site of RNA, I want to perform an umbrella sampling with spherical coordinate (r) as reaction coordinate. Specifically, In pulling simulation, I want to pull the metal ion from the origin site to outside of RNA with only