[gmx-users] Simulations box type

Hello All, I am here not with a problem but still i need your suggestions. I have a linear DNA molecule of 200nm in length and want to rum MD to calculate some bending properties. I want to know ...what kind of solvation box type will be good for such molecule?? Thank you cheers Raghav -- gmx-

[gmx-users] -vsite in Umbrella sampling

Hello Fellow Users, I have a question regarding US simulation. I am interested to know that can I treat hydrogens as virtual sites in US simulations?? I have very large protein complexes and to use higher time stepping during simulations...I am thinking to use -vsite option. what do you guys sugg

[gmx-users] SMD : pulling both primes of DNA

Hello All, My simulation system is composed of DNA and want to pull both of the primes at the same time towards each other. I have tried every possible set of parameters in pull code...and i am not able to pull them together. it's like ... the DNA molecule is aligned along Y-axis and if want to p

[gmx-users] pull code - constraint pulling - forces are zeros

Hello Fellow Users, I am trying to pull a DNA molecule. I have fixed one end and trying to pull the other one using this .mdp file.. force output is all zeros. I have tried going through the user-list but have not found any solution yet. I am using gmx-version 4.5.5. Any idea why is it happening.

[gmx-users] constant velocity pulling/Umbrella sampling

Hello Fellow Users, I have a doubt about the mdp option in case of constant velocity pulling / Umbrella pulling simulation. pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance >

[gmx-users] Gromacs-CPMD ....versions???

Hello Fellow Users, I wanted to know about the gromacs versions compatible with interfacing ...with CPMD QM/MM...??? is that particular version provided by Dr. Biswas is the only one or the latest versions are also capable of doing so??? Any News or info..or way??? Thank you all cheers Raghav

[gmx-users] want to remove H5T entry form HDB file / open terminal (P, O) for polymerization of i-motif

gt; Today's Topics: > > 1. Re: Using new atom types (Fabian Casteblanco) > 2. Re: Re: Using new atom types (Justin A. Lemkul) > 3. Re: gmx-users Digest, Vol 87, Issue 44 (raghav singh) > 4. want to remove H5T entry form HDB file / open terminal (P, O) > for polymeriz

[gmx-users] want to remove H5T entry form HDB file / open terminal (P, O) for polymerization of i-motif

Hi Justin, Yeah I have to remove that H from the that position to make my P open to contact with the O atom of the next unit. ..but if you make some precise suggestion that How can I remove that entry.. because I have tried to remove the entry from .RTP and .HDB files and in that case it starts gi

[gmx-users] Re: gmx-users Digest, Vol 87, Issue 44

Hi Justin, Yeah I have to remove that H from the that position to make my P open to contact with the O atom of the next unit. ..but if you make some precise suggestion that How can I remove that entry.. because I have tried to remove the entry from .RTP and .HDB files and in that case it starts gi

[gmx-users] Simulation of Primed DNA

Dear Experts, Hi from a beginner in Gromacs, I am trying to simulate i-motif so I have primed all the four chains and manually created a phosphodiester bond between two i-motif units. all the with Amber/Gromos ff the problem is : Fatal error: Atom P in residue DT 1 was not found in rtp entry DT