Re: [gmx-users] Questions about GB parameters

Hi! I did some digging and think I can clarify at least the first question. Sorry for the confusion with regard to the earlier post. What is specified in the gbsa.itp file under the gbr column is indeed vdW-radii. These are used to compute Born radii, as the manual says. The dielectric offset

Re: [gmx-users] xvg plotting

Hi there, in gnuplot you can do: gnuplotset datafile commentschars #% gnuplotfile(i) = sprintf(fio%d.xvg,i) gnuplotplot for[i=1:6] file(i) u 1:2 w lp in order to plot fio1.xvg fio2.xvg fio3.xvg fio4.xvg fio5.xvg fio6.xvg hope it helps and On 06/22/2011 01:38 AM, Dallas Warren wrote: Any

Re: [gmx-users] Re: local pressure v4.5 issues

How large is the number? Does the large number converges? Lateral pressure is usually large (positive or negative) at the water-hydrophobic interface. e.g., see figures in this paper: J. Am. Chem. Soc. 2011, 133, 3720–3723. Cheers, Jianguo From: Amit

[gmx-users] DPPC temperatur setting

Hi everybody I am starting to analyze the membrane system composed with DPPC lipids, I saw both MD membrane paper and KALP-15 tutorial to setting a 323K. My question is That in this way we working around 50 C, which is not body temperature 37 C, this is not realistic approach, If my interest is

Re: [gmx-users] PMF and appending simulation: -pf and -px flags (gromacs 4.0.7)

Shay Teaching wrote: Hi everyone, Does the appending option also work when doing PMF? I have a simulation that crashed in the middle (not-gromacs-related), and now I want to continue from where it stopped. But using the -append option does not seem to continue writing to the files specified

[gmx-users] in preparation for 4.5.5 and 4.6 releases

Hi, We are preparing for a new maintenance release 4.5.5. It will fix critical open issues with previous releases, so please file your reports in redmine.gromacs.org by the end of June. After the 4.5.5 release, the stable branch will be frozen for bugfixes only, and new functionality will

[gmx-users] plateau in msd (glass transition); ref_t

Hi everyone, I'm simulating a bead-spring polymer model (1600 chains and 10 beads per chain in a 26.6^3 box with pbc) with LJ and FENE potentials. I calculate the mean-square-displacement for different temperatures. For T=0.46 (in LJ units) I expected to get a plateau in the msd curve (glass

Re: [gmx-users] Programs to add residues

On Tue, Jun 21, 2011 at 4:12 PM, Chris Neale chris.ne...@utoronto.cawrote: Try Loopy. You can get it to build termini in addition to loops. http://wiki.c2b2.columbia.edu/**honiglab_public/index.php/**Software:Loopyhttp://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Loopy I've

Re: [gmx-users] Autocorrelation of dipole moment

sure, the ACF for a vector gives you the average cosine between that vector at time t=0 and the same vector at a later time lag, thus negative values may be seen as an inversion of the direction to which the vector points out (-1 would be the value for a vector lying 180 degrees away from the

Re: [gmx-users] Questions about GB parameters

Per Larsson wrote: Hi! I did some digging and think I can clarify at least the first question. Sorry for the confusion with regard to the earlier post. What is specified in the gbsa.itp file under the gbr column is indeed vdW-radii. These are used to compute Born radii, as the manual says.

[gmx-users] restraints in PMF (Justin's tutorial)

Hello, I am trying to obtain the PMF from Umbrella Sampling of the process of separating two monomers of a dimer, following Justin 's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html I have done the Umbrella Sampling simulations without

Re: [gmx-users] restraints in PMF (Justin's tutorial)

Rebeca García Fandiño wrote: Hello, I am trying to obtain the PMF from Umbrella Sampling of the process of separating two monomers of a dimer, following Justin 's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html I have done the Umbrella

[gmx-users] Re: Re:NVT equilibration of DMSO solvent (Charmm all-atom force field)

Dear Mark Abraham, Thank you for the reply. However, I am sorry to tell you that I could not find a tutorial that really is explicit to explain the procedure. Could you please suggest some tutorial covering the non-water solvent box generation and optimization using all-atom charmm force-field

RE: [gmx-users] restraints in PMF (Justin's tutorial)

Thanks a lot for your quick answer! I think they are separated enough, however my monomers are cyclic (like discs); I start with a parallel conformation between then, but along the Umbrella simulation, both of them rotate and approach. If I do not use restraints, how could I avoid the

Re: [gmx-users] restraints in PMF (Justin's tutorial)

Rebeca García Fandiño wrote: Thanks a lot for your quick answer! I think they are separated enough, however my monomers are cyclic (like discs); I start with a parallel conformation between then, but along the Umbrella simulation, both of them rotate and approach. If I do not use

Re: [gmx-users] Re: Re:NVT equilibration of DMSO solvent (Charmm all-atom force field)

udaya kiran marelli wrote: Dear Mark Abraham, Thank you for the reply. However, I am sorry to tell you that I could not find a tutorial that really is explicit to explain the procedure. Could you please suggest some tutorial covering the non-water solvent box generation and optimization

RE: [gmx-users] restraints in PMF (Justin's tutorial)

OK, I will try to increase the distances of the c.o.m of both molecules to eliminate any contact between them, adding more windows. Thanks a lot for your help! Best wishes, Rebeca. Date: Wed, 22 Jun 2011 11:51:36 -0400 From: jalem...@vt.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users]

[gmx-users] restraints in PMF (Justin's tutorial)

Actually, this depends on what you are trying to achieve. If you simply want to obtain the standard binding free energy, and somehow you know that the bound state is represented by your umbrella at dist=0 (via a crystal structure, for example), then using additional restraints is common,

[gmx-users] Re: gmx-users Digest, Vol 86, Issue 138

in master The plan is to have 4.5.5 around end of July, and 4.6-gamma a month later. Rossen -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110622/a55f081a/attachment-0001.html

Re: [gmx-users] DPPC temperatur setting

marco miele wrote: Please heed this: When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... ...and don't reply to the entire digest. I just stated the reasons a few minutes ago and won't bother to repeat myself again here.

[gmx-users] Timing variability

Dear Users: Has anybody else looked at simulation speed (ns/day) over the segments of long runs? I always benchmark and optimize my systems carefully, but it was only recently that I realized how much variability I am obtaining over long runs. Perhaps this is specific to my cluster,

Re: [gmx-users] Timing variability

On 23/06/2011 2:32 AM, chris.ne...@utoronto.ca wrote: Dear Users: Has anybody else looked at simulation speed (ns/day) over the segments of long runs? I always benchmark and optimize my systems carefully, but it was only recently that I realized how much variability I am obtaining over long

[gmx-users] Trajectory and ED - (not old question again)

Dear users, I did ED analysis for one of the trajectories, when I visualised the trajectory along the first five eigen vectors using g_nmtraj it does not show much movements. It was a simulation of 100 ns. My doubt is when I visualise the trajectory in pymol calculated just after simulation I

[gmx-users]Question about reduced unit for coarse grain

Dear all: I see from the user's manual that if our input is in reduced unit, the output will also be in reduced unit(, ftp://ftp.gromacs.org/pub/manual/3.1/manual-a4-3.1.1.pdf), P25. On the contrary, if we use standard unit, the out put will be in standard unit. This brings the

[gmx-users] Relaxed frozen groups

Hi all- Is it possible to freeze a group of atoms only partially in a direction? For instance, could I freeze a group inside a box of a definite size? Sincere thanks, Zack -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] Relaxed frozen groups

Zack Scholl wrote: Hi all- Is it possible to freeze a group of atoms only partially in a direction? For instance, could I freeze a group inside a box of a definite size? Not by defining a box, as such, but you can freeze any subset of atoms with a suitable index file that defines the

[gmx-users]Question about reduced unit for coarse grain

Dear all: I see from the user's manual that if our input is in reduced unit, the output will also be in reduced unit(, ftp://ftp.gromacs.org/pub/manual/3.1/manual-a4-3.1.1.pdf), P25. On the contrary, if we use standard unit, the out put will be in standard unit. This brings the

Re: [gmx-users] Autocorrelation of dipole moment

Thank you. If I apply an electric field will I be able to get only positive values? Regards, Chathurika. 2011/6/22 André Farias de Moura mo...@ufscar.br sure, the ACF for a vector gives you the average cosine between that vector at time t=0 and the same vector at a later time lag, thus

Re: [gmx-users]Question about reduced unit for coarse grain

Hi, The unit in output is in assumed to be for the standard unit input while the value is in reduced unit. So you need to do your own calculation to figure out what's the reduced unit is. Regards, Yang Ye On Thu, Jun 23, 2011 at 5:48 AM, Ye Yang knightyang...@gmail.com wrote: Dear all:

Re: [gmx-users]Question about reduced unit for coarse grain

Hi, Thanks for replying, Yang. But I still did not get it fully: 1. So if we use reduced unit in input, the output and calculation is still assumed to be in standard units? But the calculation itself is different since the constants are different, so the result must differed a lot.

[gmx-users] T-A mutation for a dimer protein

Dear Lishan: First, it would be great to see some evidence that you have tried to do this yourself before posting. Your I think makes it a possible waste of time for us to suggest a resolution to a problem that may or may not exist. Second, if indeed it is a problem, perhaps you could

Re: [gmx-users] T-A mutation for a dimer protein

On 23/06/2011 9:48 AM, yaoli...@msu.edu wrote: Hi All, I have a protein dimer and I want to calculate a T to A mutation free energy change using TI method. Since it is a dimer, it is very convenient (and advantageous) to mutate the T in both monomer simultaneously. Gromacs will write out

Re: [gmx-users]Question about reduced unit for coarse grain

On 23/06/2011 10:36 AM, Ye Yang wrote: Hi, Thanks for replying, Yang. But I still did not get it fully: 1. So if we use reduced unit in input, the output and calculation is still assumed to be in standard units? The calculation uses the same algorithm and whatever values you

[gmx-users] Re: T-A mutation for a dimer protein

Dear Chris and Mark, Thank you both for the response. I did the simulation already and Gromacs only gives me the total dH/dl. The two mutated sites are more than 20A alway from each other which makes it safe to assume that the interaction between the two sites is small. If I can extract

Re: [gmx-users]Question about reduced unit for coarse grain

Thank you very much, Mark. Is there anyway I can know the unit of input from the top file? I am not sure what I am getting from the webtool, although it shows kj/mol the instruction on the web says the unit is reduced unit, which makes me confused. In the former case I do not need to convert, but

Re: [gmx-users]Question about reduced unit for coarse grain

Ye Yang wrote: Thank you very much, Mark. Is there anyway I can know the unit of input from the top file? I am not sure what I am getting from the webtool, although it shows kj/mol the instruction on the web says the unit is reduced unit, which makes me confused. In the former case I do

Re: [gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water?

Dear Justin and gmxers Thank you so much for your helpful hints, but I am wondering how to check if I have obtained proper distributions for the desired ensemble, as suggested in your email? My thoughts are: 1. As for NVT ensemble, I need to check if the velocity (or speed) of molecules in my

RE: [gmx-users] Fw: properdihedrals

Could you clarify your question?? Do you want to change the default dihedrals of Gromacs to RB dihedral potential and to Furiour function? If so check the Gromacs manual for 4.5, pages 72-74. Cheers, Emanuel = Emanuel Birru PhD

Re: [gmx-users] Re: T-A mutation for a dimer protein

On 23/06/2011 12:22 PM, Lishan Yao wrote: Dear Chris and Mark, Thank you both for the response. I did the simulation already and Gromacs only gives me the total dH/dl. So what's wrong with dividing by two, like I suggested last time? You've got two events and you assert that they're

Re: [gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water?

On 23/06/2011 12:38 PM, xiaodong huang wrote: Dear Justin and gmxers Thank you so much for your helpful hints, but I am wondering how to check if I have obtained proper distributions for the desired ensemble, as suggested in your email? My thoughts are: 1. As for NVT ensemble, I need to check

Re: [gmx-users] How to set proper temperature and pressure coupling parameters, especially when using solvents other than water?

xiaodong huang wrote: Dear Justin and gmxers Thank you so much for your helpful hints, but I am wondering how to check if I have obtained proper distributions for the desired ensemble, as suggested in your email? My thoughts are: 1. As for NVT ensemble, I need to check if the velocity (or

Re: [gmx-users]Question about reduced unit for coarse grain

Ye Yang wrote: Just no reply from them for some time... Well, that's unfortunate. I'd hazard a guess that all the units are reduced, but that's just a hunch. Theoretically, all your input and output should be in reduced units. My hunch is based on the fact that everything shown (in

Re: [gmx-users]Question about reduced unit for coarse grain

Thank you very much! I will check with them carefully. Ye 2011/6/23 Justin A. Lemkul jalem...@vt.edu Ye Yang wrote: Just no reply from them for some time... Well, that's unfortunate. I'd hazard a guess that all the units are reduced, but that's just a hunch. Theoretically, all your

[gmx-users] Box-dimensions -g_energy_output

Dear users, In one of the simulations while calculating box dimensions using g_energy this output was obtained - Statistics over 5001 steps [ 0. through 10. ps ], 3 data sets All statistics are over 1978700 points Energy Average Err.Est. RMSD

[gmx-users] Re: gmx-users Digest, Vol 86, Issue 143

as this. Why is this? Thank you With Regards M. Kavyashree -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110622/25496797/attachment-0001.html -- Message: 5 Date: Wed

[gmx-users] Regarding ffG43a1p force field

Hi, I want to simulate a docked complex of my protein (GFP) with phosphotyrosine. I have found this - ffG43a1p forcefield contains parameters for pTYR, so I want to know how good is this FF for simulating my system... As in the literature its mentioned that people have used CHARMM, AMBER, OPLS ff

Re: [gmx-users] Regarding ffG43a1p force field

Hi Bharat, I used Amber force field, but still i am not statisfied with the parameters which i used because after some nanosecond simulation(1 -2 ns) the planarity of the sturcture changes. I tired changing the force constant but still not much successfull. If you got success please let me

Re: [gmx-users] Regarding ffG43a1p force field

Hi Sir, Actually I am doing the simulation without the chromophore. So, planarity does not matter to be .. On Thu, Jun 23, 2011 at 2:23 PM, Ramachandran G gtr...@gmail.com wrote: Hi Bharat, I used Amber force field, but still i am not statisfied with the parameters which i used because

Re: [gmx-users] Regarding ffG43a1p force field

Why you are doing simulation without chromophore? Chromophore is important in GFP. If you want i can send you the forcefield which i am using for GFP. Rama On Wed, Jun 22, 2011 at 10:29 PM, bharat gupta bharat.85.m...@gmail.comwrote: Hi Sir, Actually I am doing the simulation without the