Re: [gmx-users] error in phosphoserine simulation during MD

On 6/17/17 4:05 PM, marzieh dehghan wrote: Hi Dear all I want to simulate a protein containing phosphoserine using MD, so I place the force field into the working directory and modified all parameters of force field for example SEP (phosphoserine) was added as Protein in the residuestypes.dat

[gmx-users] error in phosphoserine simulation during MD

Hi Dear all I want to simulate a protein containing phosphoserine using MD, so I place the force field into the working directory and modified all parameters of force field for example SEP (phosphoserine) was added as Protein in the residuestypes.dat , but I confronted the following error? Atom

Re: [gmx-users] FLUCTUATION IN DISTANCE

On 6/17/17 11:47 AM, Neha Gupta wrote: Hi gromacs users, How to examine the fluctuation in distance in protein ligand binding, between protein residue and the ligand? What is the exact command ? Read about how to use gmx distance. Then perform statistical analysis on the time series. -

Re: [gmx-users] How to create parameters for polyethyleneglycol (PEG) 6000 in a gromacs MD simulation

On 6/17/17 8:55 AM, Sajeewa Pemasinghe wrote: Hi all, I have to carry out MD simulations involving PEG 6000 molecules. When I first build this it is a very long (~480 Angstrom) linear chain. I have the bond/angle/dihedral parameters for this linear structure. Usually when I introduce a non-sta

[gmx-users] FLUCTUATION IN DISTANCE

Hi gromacs users, How to examine the fluctuation in distance in protein ligand binding, between protein residue and the ligand? What is the exact command ? Thanks, Neha -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List bef

Re: [gmx-users] using groups in index for gmx select

Hi, I don't know, but like all kinds of complex things, start with a simple thing and add complexity. Can you get the input index group to be the output group? Mark On Wed, 14 Jun 2017 07:45 Sahithya S Iyer wrote: > Hi gmx users, > > Can anyone please tell me how to use a group in index file i

Re: [gmx-users] using groups in index for gmx select

Hi, >Basically I would like to select oxygen atoms of water molecules that are >2 nm around the phosphate groups of one monolayer. There is Tcl script available in NAMD for selecting the oxygen atoms of water molecules that are XX nm around XXX. Sorry, I don't have the link, but you can easily g

[gmx-users] How to create parameters for polyethyleneglycol (PEG) 6000 in a gromacs MD simulation

Hi all, I have to carry out MD simulations involving PEG 6000 molecules. When I first build this it is a very long (~480 Angstrom) linear chain. I have the bond/angle/dihedral parameters for this linear structure. Usually when I introduce a non-standard residue, I perform an optimization in Gaussi

Re: [gmx-users] System reaches ~124K after simulated annealing upto 300K (Justin Lemkul)

On 6/17/17 2:23 AM, Apramita Chand wrote: Dear Justin, The normal (non-annealing) equilibration works fine. 100ps of NVT and it easily reaches 300K. There are no error messages. Am I doing the simulated annealing correctly? Looks fine, other than generating velocities at 300 K but specifying