Re: [gmx-users] Questions about the MFFA boundery implementation of Gromacs?

It is not clear what you are asking. Could you try to reformulate your problem/question? Did you read the Louhivuori-PNAS papers? There are lots of details in the supplementary material. On Apr 27, 2013, at 6:43, "song.yongshun" wrote: > Dear all: > I was using the MFFA version of Gromacs w

[gmx-users] RE: How to rescue trr trajectory when two or more corrupted frames exist

Thanks for the reply Chris :). It is not possible to get the data with -b option, since trjconv crashes when it meets the corrupted frame. I never had corruption issues in the past and thereby didn't use gmxcheck early enough to avoid the second corruption. The problems should have occurred in

Re:Re: [gmx-users] Questions about the MFFA boundary implementation of Gromacs?

I have read the paper of "Application of Mean Field Boundary Potentials in Simulations of Lipid Vesicles" carefully ,and I have just read the Louhivuori-PNAS paper. However,I didn't find what I want. I will make the question clear. In the paper,it said " In order to resolve this issue, artific

Re: [gmx-users] ATP/Mg+2 parameters

Hello George, What do you mean by "best"? It really depends on the force-field that you are using/intend to use. Best, João On Fri, Apr 26, 2013 at 4:00 PM, George Patargias wrote: > Hello > > Doe anybody know what is the "best" (the most suitable) set of parameters > to use for ATP/Mg+2 ? > >

[gmx-users] Genion cannot read from input

I am running genion neutralize the charge of my protein. I got an error that wasn't very descriptive Fatal error: Cannot read from input The part of the script that called this program read as follows /usr/local/gromacs-4.5.5/bin/grompp -f em.mdp -c filled_box.pdb -p protein_mod_filled5.top -o ions

[gmx-users] Calculation of helicity of alpha-helix which is parallel to X-axis

Hi, I want to calculate helicity of an alpha-helix which is parallel along X-axis. But, during usage of g_helix command its manual showing it will calculate helicity of alpha-helix which is parallel to Z-axis. So, please tell me the solution. Thanking you, Sujit -- gmx-users mailing list

Re: [gmx-users] Calculation of helicity of alpha-helix which is parallel to X-axis

On 4/27/13 11:43 AM, Sujit Sarkar wrote: Hi, I want to calculate helicity of an alpha-helix which is parallel along X-axis. But, during usage of g_helix command its manual showing it will calculate helicity of alpha-helix which is parallel to Z-axis. So, please tell me the solution. Use t

Re: [gmx-users] Genion cannot read from input

On 4/27/13 11:21 AM, Nathan Bullock wrote: I am running genion neutralize the charge of my protein. I got an error that wasn't very descriptive Fatal error: Cannot read from input The part of the script that called this program read as follows /usr/local/gromacs-4.5.5/bin/grompp -f em.mdp -c fi

Re: [gmx-users] Genion cannot read from input

On 4/27/13 12:28 PM, Justin Lemkul wrote: On 4/27/13 11:21 AM, Nathan Bullock wrote: I am running genion neutralize the charge of my protein. I got an error that wasn't very descriptive Fatal error: Cannot read from input The part of the script that called this program read as follows /usr/l

[gmx-users] Including polarizability by a Drude oscillator or the shell model

Hi, I am interested in including polarizability using a Drude harmonic oscillator ("charge on a spring"). In section 3.5 of the version 4.5.4 manual, "Shell molecular dynamics" is described briefly. It seems that the shell model is quite similar, if not identical, to the Drude oscillator. Howev

[gmx-users] Re: Genion cannot read from input

So I need to provide a group for the function genion, in the example you provided g-energy has several group names. Where do I find the group names for genion? - Graduate Student University of Iowa Cheatum Research Group -- View this message in context: http://gromacs.5086.x6.nabble.com/G

Re: [gmx-users] Re: Genion cannot read from input

On 4/27/13 2:52 PM, Nathan Bullock wrote: So I need to provide a group for the function genion, in the example you provided g-energy has several group names. Where do I find the group names for genion? Group selection is the same for every Gromacs program. Select by name or number. Run ge

[gmx-users] Re: Genion cannot read from input

I created a text file called choices with the number corresponding to the ions group. I then had the text file as an argument for the genion function. I still got the same input error. - Graduate Student University of Iowa Cheatum Research Group -- View this message in context: http://grom

[gmx-users] Re: Genion cannot read from input

The useful part of the error file -f em.mdp Inputgrompp input file with MD parameters -po mdout.mdp Output grompp input file with MD parameters -c filled_box.pdb InputStructure file: gro g96 pdb

Re: [gmx-users] GPU efficiency question

Probably the part of the calculation done on the GPU is not rate limiting. There's no point having four chefs to make one dish... Look at the beginning and end of your .log files for diagnostic information. If this is a single node, you should be using threadMPI, not real MPI. Generally four CPU c

Re: [gmx-users] Re: Genion cannot read from input

On Sat, Apr 27, 2013 at 10:25 PM, Nathan Bullock wrote: > I created a text file called choices with the number corresponding to the > ions group. I then had the text file as an argument for the genion > function. > That cannot work. Read the link Justin provided. Mark > I still got the same i

Re: [gmx-users] Re: Genion cannot read from input

The problem is that genion is expecting input from the command line, telling it which molecules to replace with ions - usually SOL. If you are running a script you have to script an input line for genion. Warren Gallin On 2013-04-27, at 2:56 PM, Nathan Bullock wrote: > The useful part of the

Re: [gmx-users] How to rescue trr trajectory when two or more corrupted frames exist

AFAIK there is no magic number header. However, .trr files have frames of constant size, so you can make a .tpr that will write a .trr file that will include the longest period of your nst[xfv]out. Some Unix tool like dd (or maybe hexdump) can probably tell you the size of that repeating unit. Then

Re: [gmx-users] Using virtual site

On Fri, Apr 26, 2013 at 6:16 PM, 라지브간디 wrote: > Dear gmx, > > > I am having a trouble in setting the virtual site on CO molecule. > > > When I use V-site for CO, it end up with energy minimization error as > follows: > > > > > steepest Descents: >Tolerance (Fmax) = 1.0e+03 >Number

[gmx-users] How to rescue trr trajectory when two or more corrupted frames exist

This is great advice from Mark. If you don't get around to doing analysis frequently, then you can at least set up your run script to execute gmxcheck on all relevant files prior to each time you restart a run in which you load in a .cpt file and to error out if there is some corruption found.