Re: [gmx-users] Using Charmm FF with implicit solvent on gromacs

Hi! Currently it is not possible to use GBSW in Gromacs. As you noted, there are three GB-models available (Still,HCT,OBC), that can be run using plain cutoffs (or no cutoffs at all, using the optimized all-vs-all kernels). Currently there is unfortunately no work being done to extend the range

[gmx-users] Pairwise forces

Dear all, I know similar topics have already been discussed, but there is a question regarding pairwise forces that could not be resolved by reading the mailing list. Our group has already done some rather long simulations and according to the script files forces are written every 1 step

[gmx-users] Role of epsilon_rf in implicit solvation

Dear users, I've got yet another question about the implicit solvent models used in Gromacs. I saw in some simulations that epsilon_rf was set to 0 meaning infinite dielectric constant. The manual is not clear about this, since it is mentioned in combination with reaction field only. So is t

Re: [gmx-users] Role of epsilon_rf in implicit solvation

Hi! It would be nice to have reaction-field for GB as well, but currently this is not the case. The polarisation energy is scaled using (1.0/epsilon_r - 1.0/gb_epsilon_solvent) always, epsilon_rf is never used. Cheers /Per 19 nov 2010 kl. 12.30 skrev Christian Mücksch: > So is this epsilon_

[gmx-users] question about simualtion of CNT from a rookie

Dear all, I am trying to study an infinite length CNT in SPC water box under NPT using gromacs 4.5.3. The axis of CNT is along Z direction. The options "pbc = xyz " and "periodic_molecules = yes" are included in all mdp files. The whole system was minimized first, followed by an NVT simulation. T

[gmx-users] noxvgr

Hi, Suppose when I use gyrate, I want the output to be the eps, when I tried -noxvgr -w sounds I failed to get. I do not understand it well. I can get .xvg picture, and seems the gnuplot not easy to interpret and save it as .eps or png. Any idea? Thanks and best, lina -- gmx-users mailing

Re: [gmx-users] noxvgr

#ZHAO LINA# wrote: Hi, Suppose when I use gyrate, I want the output to be the eps, The only tool that produces .eps files is xpm2ps. when I tried -noxvgr -w Is -noxvgr even a correct option? It seems like if you want non-formatted output, you should use "-xvg none" in the command lin

RE: [gmx-users] noxvgr

I suspect it might mine grace was wrong, when I tried to use save as, it has bugs, I will check this first. Thanks for your answering. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu]

Re: [gmx-users] noxvgr

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 11/19/2010 03:03 PM, #ZHAO LINA# wrote: > Hi, > > Suppose when I use gyrate, I want the output to be the eps, > > when I tried -noxvgr -w > > sounds I failed to get. > > I do not understand it well. > > I can get .xvg picture, and seems the gnu

Re: [gmx-users] noxvgr

#ZHAO LINA# wrote: I suspect it might mine grace was wrong, when I tried to use save as, it has bugs, I will check this first. Exporting to different formats is not done with "Save As" but rather "Print" (using "Print Setup" to choose the proper format). Simply saving your plot creates an

RE: [gmx-users] noxvgr

It works (cool). Thanks for both of you. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, November 19, 2010 10:23 PM To: Discussion list for GROMACS users Subject: Re: [

[gmx-users] mpdboot and mpirun hangs (not crashing)

Hi, I am trying to run my production run with mpirun and this hangs (basically stop writing any files). The processes continue to run without any output. I have to kill and restart which again hangs after some time. Does anyone have any problems with this? what I am doing is mpdboot -n

Re: [gmx-users] mpdboot and mpirun hangs (not crashing)

On 20/11/2010 2:57 AM, X Rules wrote: Hi, I am trying to run my production run with mpirun and this hangs (basically stop writing any files). The processes continue to run without any output. I have to kill and restart which again hangs after some time. Does anyone have any problems with t

Re: [gmx-users] Pairwise forces

On 19/11/2010 10:15 PM, Reiner Ribarics wrote: Dear all, I know similar topics have already been discussed, but there is a question regarding pairwise forces that could not be resolved by reading the mailing list. Our group has already done some rather long simulations and according to the

RE: [gmx-users] mpdboot and mpirun hangs (not crashing)

I am trying to check some of these issues. thanks for your help Date: Sat, 20 Nov 2010 03:38:08 +1100 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] mpdboot and mpirun hangs (not crashing) Message body On 20/11/2010 2:57 AM, X Rules w

[gmx-users] mutiple dihedral terms

Hi, I have a molecule consisting of 4 atoms 1-2-3-4 . The paper parameterizing the molecule has reported combination of following multiple set of dihedral terms by fitting the dihedral angle distributions of this tetra-atomic molecule : theta0 K n 180 1.96 1

Re: [gmx-users] mutiple dihedral terms

Sanku M wrote: Hi, I have a molecule consisting of 4 atoms 1-2-3-4 . The paper parameterizing the molecule has reported combination of following multiple set of dihedral terms by fitting the dihedral angle distributions of this tetra-atomic molecule : theta0 K n 180

[gmx-users] question regarding to PMF calculation between 2 plates

Dear GROMACS users, I have a question for calculating the potential of mean force between 2 plates (i.g., graphene) in water. It is not technically as simple as it seem. I found this question has been asked many times (I sum them up in the bottom of this note, so maybe it will be helpful for someo

Re: [gmx-users] mutiple dihedral terms

On 20/11/2010 6:40 AM, Justin A. Lemkul wrote: Sanku M wrote: Hi, I have a molecule consisting of 4 atoms 1-2-3-4 . The paper parameterizing the molecule has reported combination of following multiple set of dihedral terms by fitting the dihedral angle distributions of this tetra-atomic m

[gmx-users] disparity in RMSD calculation

Dear Users, I calculated RMSD for a trajectory with same reference structure using GROMACS and VMD. I observed completely difference plots for the same data. Please see the attached file. What could be the cause for this disparity? Thanks for any suggestion. Sunita <>-- gmx-users mailing lis

Re: [gmx-users] disparity in RMSD calculation

On Sat, Nov 20, 2010 at 12:54 AM, Sunita Patel wrote: > Dear Users, > > I calculated RMSD for a trajectory with same reference structure using > GROMACS > and VMD. I observed completely difference plots for the same data. Please > see > the attached file. > > What could be the cause for this dispa

Re: [gmx-users] disparity in RMSD calculation

On Sat, 20 Nov 2010 01:13:51 -0500, Yongchul Chung wrote > On Sat, Nov 20, 2010 at 12:54 AM, Sunita Patel > wrote: > Dear Users, > > I calculated RMSD for a trajectory with same reference structure using GROMACS > and VMD. I observed completely difference plots for the same data. Please see > th