[gmx-users] reg linear interpolation

Dear justin, Thank you for your previous reply. Can i use g_morph  tool in gromacs for wild type and mutated Pdb Because it ask two input PDB files should these two files contains equal no residues? otherwise can i use different PDB (WT and Mutated PDB )  which differ only by

[gmx-users] fatal error

Hi all Why is pull geometry direction not supported in g_wham ? I got the following error. I did this to compare with the same simulations but with pull geometry = distance. Fatal error: Pull geometry direction not supported -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Why does the -append option exist?

Hi Dimitar,Thanks for the bug report. Would you mind trying the test program I attached on the same file system that you get the truncated files on?compile it with gcc testje.c -o testioSander testje.c Description: Binary data On Jun 7, 2011, at 23:21 , Dimitar Pachov wrote:Hello,Just a quick

Re: [gmx-users] Essential dynamics - concepts

Hi Kavya, Thanks sir. I will go through them. However I have referred - A Tutorial on Principle component Analysis by  Lindsay I Smith. Which gave a good understanding about the concepts. Still I have some doubts regarding eigen values, as you have told I will think over them again. I know

[gmx-users] Gromacs-4.5.4 install error

Hi all gmx-users: I install gromacs-4.5.4, with tar xzf gromacs-4.5.4.tar.gz cd gromacs-4.5.4 export MPICC=/usr/mpi/gcc/mvapich2-1.4.1/bin/mpicc ./configure --prefix=/home/xuji/bin/gmx_4.5.4/parallel_float --enable-mpi --program-suffix=_mpi --without-x --with-fft=fftw3 --enable-all-static

[gmx-users] effect of slab geometry correction on Coulomb energies for interface systems

Hi all, I am trying to investigate how the slab geometry correction affects calculated Coulomb energies for interface systems. I have an air/water interface with a box size of 3x3x9 nm. I ran 2 independent simulations with changing ewald_geometry option: 3d (default value), and 3dc. You can find

Re: [gmx-users] reg linear interpolation

vidhya sankar wrote: Dear justin, Thank you for your previous reply. Can i use g_morph tool in gromacs for wild type and mutated Pdb Because it ask two input PDB files should these two files contains equal no residues? otherwise can i use different PDB (WT and Mutated PDB )

[gmx-users] distance/direction PMF

Hi all Could someone please get back to me on this. I have ran two sets of umbrella sampling simulations 1- Using pull_geometry = distance, and pull_dim = Y Y Y 2- Using pull_geometry = direction, with pull_vec = 0.462808 0.494125 0.735968 In both cases I wish to calculate the PMF for taking a

[gmx-users] problem in g_density

Hi, The simulation box consists of layers of cyclohexane and vacuum. Ensemble is NVT. The density profiles of cyclohexane for 5-10 ns, 10-15 ns and 15-20 ns coincide. However the density profile for 5-20 ns is significantly higher than the ones calculated. g_density -n -b 5000 -e 2 If

Re: [gmx-users] problem in g_density

On 8/06/2011 9:41 PM, cdalgicdir wrote: Hi, The simulation box consists of layers of cyclohexane and vacuum. Ensemble is NVT. The density profiles of cyclohexane for 5-10 ns, 10-15 ns and 15-20 ns coincide. However the density profile for 5-20 ns is significantly higher than the ones

[gmx-users] Re: distance/direction PMF

Gavin Melaugh wrote: Hi all Could someone please get back to me on this. I have ran two sets of umbrella sampling simulations 1- Using pull_geometry = distance, and pull_dim = Y Y Y 2- Using pull_geometry = direction, with pull_vec = 0.462808 0.494125 0.735968 In both cases I wish to

Re: [gmx-users] oplsaa vs. charmm

Dear Prof van der Spoel and GROMACS users, I have read the article Scrutinizing Molecular Mechanics Force Fields... where it is demonstrated that AMBER99sb yields protein conformations that are in better agreement with residual dipolar coupling, J-coupling and NOE data, compared with other force

Re: [gmx-users] Re: distance/direction PMF

Gavin Melaugh wrote: Hi Justin Many thanks for the reply I know technically I am doing two different things. However due to my starting conifgurations in both cases I would expect similar results. Could you confirm the following points 1) In pull_geometry=distance, and pull_dim =YYY; is the

[gmx-users] g_hbond/g_sas - how is it calculated?

Hi, I have a question related to the calculation of hydrogen bonds in Gromacs. As I read in Manual it comes from the distance between donor and acceptor ( = 0.35 nm) and the angle =30 degr beween hydrogen and acceptor. The question is - why 30 degr? How is it related to the reality? The

Re: [gmx-users] g_hbond/g_sas - how is it calculated?

On Wed, Jun 8, 2011 at 10:20 PM, Marzinek, Jan j.marzine...@imperial.ac.uk wrote: Hi, I have a question related to the calculation of hydrogen bonds in Gromacs. As I read in Manual it comes from the distance between donor and acceptor ( = 0.35 nm) and the angle =30 degr beween hydrogen and

Re: [gmx-users] g_hbond/g_sas - how is it calculated?

Marzinek, Jan wrote: Hi, I have a question related to the calculation of hydrogen bonds in Gromacs. As I read in Manual it comes from the distance between donor and acceptor ( = 0.35 nm) and the angle =30 degr beween hydrogen and acceptor. The question is - why 30 degr? How is it

Re: [gmx-users] Re: distance/direction PMF

Justin I did a short test on a particular window with the specified vector with pull_init =0.78nm. I then grompp(ed) the final configuration and it gave me a distance of 0.78 as the initial ditsance, fair enough. However when I viewed the final line from g_dist the absolute distance or modulus

Re: [gmx-users] Re: distance/direction PMF

Gavin Melaugh wrote: Justin I did a short test on a particular window with the specified vector with pull_init =0.78nm. I then grompp(ed) the final configuration and it gave me a distance of 0.78 as the initial ditsance, fair enough. However when I viewed the final line from g_dist the

[gmx-users] (no subject)

Hello everybody, I was wondering if the gro file format somehow supports systems that are greater than 9 molecules (not atoms), since the first column is fixed to size 5. Anybody know a way around this problem? I've tried working with pdb, but GROMACS seems to ignore all entries with

Re: [gmx-users] (no subject)

Sven Benson wrote: Hello everybody, I was wondering if the gro file format somehow supports systems that are greater than 9 molecules (not atoms), since the first column is fixed to size 5. Anybody know a way around this problem? I've tried working with pdb, but GROMACS seems to

Re: [gmx-users] Re: distance/direction PMF

Hi Justin Sorry maybe I was unclear before with my first point; the specified distance in the mdp file is 0.78nm, which grompp returns back as the ref distance. The distance at the start that grompp returns is also 0.78nm, even though the actual distance is 0.815nm. That's why I was asking what

[gmx-users] Question about umbrella sampling pull-geometry option

Dear GMXers, I'm running umbrella PMF calculations using GROMACS 4.5. A molecule is placed at various locations of a channel to compute the energy barrier of the entrance. Below is the PMF section of mdp input, to compute the PMF around the position of (4.04700, 4.0582, -2.2058). The pulling

[gmx-users] a question about position restraint time for long alkyl chain molecules

Hi there I put a SDS Spherical micelle in solution and want to apply position restraint before mdrun. Here I have a question: For macromolecules like micelles, should the position restraint apply to not only the water molecules (and ions) but also to the surfactant molecules in the micelle? If it

Re: [gmx-users] Re: distance/direction PMF

Gavin Melaugh wrote: Hi Justin Sorry maybe I was unclear before with my first point; the specified distance in the mdp file is 0.78nm, which grompp returns back as the ref distance. The distance at the start that grompp returns is also 0.78nm, even though the actual distance is 0.815nm.

Re: [gmx-users] Question about umbrella sampling pull-geometry option

WU Yanbin wrote: Dear GMXers, I'm running umbrella PMF calculations using GROMACS 4.5. A molecule is placed at various locations of a channel to compute the energy barrier of the entrance. Below is the PMF section of mdp input, to compute the PMF around the position of (4.04700, 4.0582,

Re: [gmx-users] a question about position restraint time for long alkyl chain molecules

XUEMING TANG wrote: Hi there I put a SDS Spherical micelle in solution and want to apply position restraint before mdrun. Here I have a question: For macromolecules like micelles, should the position restraint apply to not only the water molecules (and ions) but also to the surfactant

[gmx-users] Calculation of unsaturated deuterium order parameters for POPC

Hi Everyone, I am facing a problem when calculating the lipid deuterium order parameters for the unsaturated carbons of the sn-2 tail of POPC using g_order with GROMACS version 4.5.4 (although I have tried other older versions too but they all give the same results). Firstly, I should say

Re: [gmx-users] Re: distance/direction PMF

Yeah I set pull_init =0, and pull_start = yes, and it still gave a distance at start as 0.78nm. It must be doing something funny because with pull_vec, because when I use pull_geometry = distance and pull_dim = Y Y Y, the distance 0.815nm is returned as the distance at start, which is the actual

Re: [gmx-users] a question about position restraint time for long alkyl chain molecules

Hi Justin Sorry I did not explain clearly. I apply position restraint to the head group of surfactant molecules and let all others (solvents and tail of surfactants) run freely. I am concerning about how long I should restraint the head group of surfactant molecules. If only concerning the

Re: [gmx-users] a question about position restraint time for long alkyl chain molecules

XUEMING TANG wrote: Hi Justin Sorry I did not explain clearly. I apply position restraint to the head group of surfactant molecules and let all others (solvents and tail of surfactants) run freely. I am concerning about how long I should restraint the head group of surfactant molecules. If

Re: [gmx-users] Why does the -append option exist?

Hello, On Wed, Jun 8, 2011 at 4:21 AM, Sander Pronk pr...@cbr.su.se wrote: Hi Dimitar, Thanks for the bug report. Would you mind trying the test program I attached on the same file system that you get the truncated files on? compile it with gcc testje.c -o testio Yes, but no problem:

Re: [gmx-users] Re: distance/direction PMF

Gavin Melaugh wrote: Yeah I set pull_init =0, and pull_start = yes, and it still gave a distance at start as 0.78nm. It must be doing something funny because with pull_vec, because when I use pull_geometry = distance and pull_dim = Y Y Y, the distance 0.815nm is returned as the distance at

Re: [gmx-users] a question about position restraint time for long alkyl chain molecules

Got it (cool :)), Thank you!!! Best! Xueming On Wed, Jun 8, 2011 at 1:15 PM, Justin A. Lemkul jalem...@vt.edu wrote: XUEMING TANG wrote: Hi Justin Sorry I did not explain clearly. I apply position restraint to the head group of surfactant molecules and let all others (solvents and tail

Re: [gmx-users] oplsaa vs. charmm

Do you have some experimental data to compare to your IDP simulations, like X-ray scattering or some such? I'd imagine that IDP simulations with either forcefield would only be qualitatively accurate given that the forcefields are calibrated, as you say, on rigid

Re: [gmx-users] oplsaa vs. charmm

I really don't think you can get adequate sampling for IDPs that have 40 residues, using full atomic MD. On Wed, Jun 8, 2011 at 3:25 PM, Michael Daily mdaily.w...@gmail.com wrote: Do you have some experimental data to compare to your IDP simulations, like X-ray scattering or some such? I'd

Re: [gmx-users] oplsaa vs. charmm

Da-Wei Li wrote: I really don't think you can get adequate sampling for IDPs that have 40 residues, using full atomic MD. I disagree. Perhaps brute force MD would not accomplish the task (unless you have considerable resources and don't want your answers very quickly, but even then...),

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

thomas, i've recently placed a similar question and justin asked me to show my index for the double bound calculation, so, i'm asking you the same. you should have Ci-1 Ci - the first carbon of the double bound Ci+1 - the second carbon of the double bound Ci+2 in that index doing this,

[gmx-users] Umbrella sampling of phosphate ion binding

Hi Justin, I am having following doubts regarding umbrella sampling of phosphate ion binding to my protein . 1. As per the tutorial, I need to fix an immobile reference. In my case which region do I have to fix as my protein consists of one single chain. Since I am studying the binding and

Re: [gmx-users] Umbrella sampling of phosphate ion binding

bharat gupta wrote: Hi Justin, I am having following doubts regarding umbrella sampling of phosphate ion binding to my protein . 1. As per the tutorial, I need to fix an immobile reference. In my case which region do I have to fix as my protein consists of one single chain. Since I am

Re: [gmx-users] Umbrella sampling of phosphate ion binding

does the gromacs force field has topology and ff parameter for H2PO4(-) ion . As I have derived both topology and FF parameter from prodrug server and after checking the topology I found that it has deleted of the hydrogen. On Thu, Jun 9, 2011 at 10:16 AM, Justin A. Lemkul jalem...@vt.edu wrote:

Re: [gmx-users] Umbrella sampling of phosphate ion binding

bharat gupta wrote: does the gromacs force field has topology and ff parameter for H2PO4(-) ion . As I have derived both topology and FF parameter from prodrug Probably not; check the .rtp file for your desired force field. server and after checking the topology I found that it has deleted

Re: [gmx-users] Umbrella sampling of phosphate ion binding

I found it in the /shared/top/ gmx.ff folder . Here's the file ; ; Force field based on GROMOS with new charges as described in ; D. van der Spoel, K.A. Feenstra, M.A. Hemminga and H.J.C. Berendsen: ; Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic ; mottle virus coat

Re: [gmx-users] Gromacs-4.5.4 install error

On 8/06/2011 7:06 PM, xuji wrote: Hi all gmx-users: Please do not cross-post such questions to gmx-developers. This question has nothing to do with development. I install gromacs-4.5.4, with tar xzf gromacs-4.5.4.tar.gz cd gromacs-4.5.4 export MPICC=/usr/mpi/gcc/mvapich2-1.4.1/bin/mpicc

Re: [gmx-users] Umbrella sampling of phosphate ion binding

bharat gupta wrote: Sorry to ask this ... If I try SMD with prodrug generated topology for the time being , will it be useful to do that ?? As I don't have much time as of now to parametrize and do SMD... That's a great way to waste time. If you run a simulation with sub-par parameters,

RE: [gmx-users] Umbrella sampling of phosphate ion binding

You have been provided there with the reference in which the parameters for the molecule were derived. Read it! And determine yourself if it is applicable or not to what you are doing and the forcefield you are using. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash

Re: [gmx-users] Umbrella sampling of phosphate ion binding

Hi, After searching I have found parameters for phosphorylated tyrosine. And my experiment also involves that as in this case phosphate ion only binds to the active site. So, can I use the parameter for umbrella sampling taken from amber parameter database. !!index array str Y1P

[gmx-users] Umbrella sampling of phosphate ion binding

What forcefield is that for? Sounds like it is more than likely one of the AMBER ones. What forcefield are you using for the rest of your system that you are simulating? Are they the same? They should be. If not, are they compatible? A minor number of them are compatible to some degree,

Re: [gmx-users] Umbrella sampling of phosphate ion binding

Actually, I am planning to use AMBER forcefield for both phosphotyrosine and for the system too. The parameters are reliable as they have been published (http://www.springerlink.com/content/u527364w03568353/fulltext.pdf) . But I want to know how to add them to the force field. I have checked the