Re: [gmx-users] QMMM

I did follow the Gaussian/Gromacs QM/MM set up guide too and was not successful. On Tue, Mar 8, 2011 at 1:28 PM, Jack Shultz jackygraha...@gmail.com wrote: Good luck. I followed the instructions and was not successful. On Tue, Mar 8, 2011 at 12:48 AM, Haresh ajanihar...@gmail.com wrote:

Re: [gmx-users] g_rms and g_cluster

Hi Justin If I make an index group with backbone and CA C N O group of the concerned residues and then do least square fitting then do this fitting is equivalent to backbone fitting first and then translating to coincide CA of the residue of interest. Is there any other programme developed for

[gmx-users] creating a bilayer of dppc

Dear gromacs users having the .gro file for the dppc monolayer, how can i create a bilayer? I am interested in making bilayer from the equilibrated monolayer which i have for dppc. what changes are necessary to be done in simulation files to start a run with the bilayer? Thanks for your time D.M

[gmx-users] membrane protein

Dear All in membrane protein tutorial: What is the P-N vector? RMSD for what group do I need to calculate? How can I estimate the helix tilt? Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] creating a bilayer of dppc

dear delara, converting the monolayer gro to pdb with editconf and then using that pdb in packmol might be a way of doing it. don't forget to adjust your *top file to the new number of items (2x) and their order. that should do it, i guess best regards, igor Igor Marques

[gmx-users] Density of water, Dispcorr and rmsd

Dear users, What is the difference between densities predicted by tip4p and spc models? I am using tip4p (with OPLSAA forcefield) in the simulation, during position restrained dynamics, Average water density is around 1015kg-m-3 at 300K which is quite far from expt value.. The Dispersion

Re: [gmx-users] g_rms and g_cluster

On 09/03/11, shahid nayeem msnay...@gmail.com wrote: Hi Justin If I make an index group with backbone and CA C N O group of the concerned residues and then do least square fitting then do this fitting is equivalent to backbone fitting first and then translating to coincide CA of the

[gmx-users] Definition of helicity

Dear all, Now I am using g_helix module to calculate helicity of each residues in protein. In the manual, there seems to be no detailed description about the definition of the helicity. Could you let me know the detail, or where should I refer to. Thank you in advance, Hiroshi

[gmx-users] Zero Potential of Mean Force with g_wham

Dear all, I am running umbrella sampling of a molecule through a lipid bilayer with gromacs 4.5.1. When I extracted the potential of mean force with g_wham I got zero for all the windows. Any ideas of why this is happening? This is the command I used: g_wham_4.5.1 -it tpr.dat -if pullf.dat -o

Re: [gmx-users] creating a bilayer of dppc

Igor Marques wrote: dear delara, converting the monolayer gro to pdb with editconf and then using that pdb in packmol might be a way of doing it. don't forget to adjust your *top file to the new number of items (2x) and their order. that should do it, i guess That might work, or

Re: [gmx-users] Density of water, Dispcorr and rmsd

On 9/03/2011 10:43 PM, Kavyashree M wrote: Dear users, What is the difference between densities predicted by tip4p and spc models? I am using tip4p (with OPLSAA forcefield) in the simulation, during position restrained dynamics, Average water density is around 1015kg-m-3 at 300K which is

Re: [gmx-users] Definition of helicity

cd...@ipc.uni-karlsruhe.de wrote: Dear all, Now I am using g_helix module to calculate helicity of each residues in protein. In the manual, there seems to be no detailed description about the definition of the helicity. Could you let me know the detail, or where should I refer to.

[gmx-users] Re: 4. Re: QMMM (Txema Mercero)

Please be more specific than not successful. And also please understand that there are two things involved: the installation, which is so complicated because the gaussian license forbids distrubution of source code. The actual QM, which sometimes is not thought through well enough. A

Re: [gmx-users] using one thermostat for entire system ??

Thanks Mark for the advice. I have just rerun a test simulation with each of my gas species coupled separately to a thermostat and have got similar values for the quantities of interest (diffusion coefficients). However I am not sure that this will satisfy the reviewer without a bit more

Re: [gmx-users] Instantaneous Square Displacement

Thanks for the advice. I has also found that last source on google and have been thinking how I could apply this. I assume that if I plotted [rt - r0]^2 against time then (for a single molecule) I would get peaks on the graph when the molecules are mobile and dips (where [rt-r0]^2 is

Re: [gmx-users] Definition of helicity

Hi Justin, Thank you for your notice. I am afraid my explanation was not enough. When protein atoms is specified, g_helix seems to calculate the helicities for all residue. And then, the helicity value of each residues is written into helicity.xvg. The value probably means how much percentage

Re: [gmx-users] Definition of helicity

On 10/03/2011 12:58 AM, cd...@ipc.uni-karlsruhe.de wrote: Hi Justin, Thank you for your notice. I am afraid my explanation was not enough. When protein atoms is specified, g_helix seems to calculate the helicities for all residue. And then, the helicity value of each residues is written

Re: [gmx-users] Definition of helicity

cd...@ipc.uni-karlsruhe.de wrote: Hi Justin, Thank you for your notice. I am afraid my explanation was not enough. When protein atoms is specified, g_helix seems to calculate the helicities for all residue. And then, the helicity value of each residues is written into helicity.xvg. The

[gmx-users] secondary structure propensities of residues

Hi, How do get the percentage of the secondary structure propensities of residues? seems dssp none such effect? Thanks for any answers. lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] Zero Potential of Mean Force with g_wham

I met the same problem when using 4.5.1 for some systems, the PMF shows zero curve, while the hist file looks fine. The problem disappears when using 4.5.2. Jianguo From: Susana Tomasio susietoma...@gmail.com To: gmx-users@gromacs.org Sent: Wednesday, 9 March

Re: [gmx-users] secondary structure propensities of residues

ZHAO Lina wrote: Hi, How do get the percentage of the secondary structure propensities of residues? seems dssp none such effect? The scout.xvg file contains everything you need (in a broad sense) - number of residues in a given secondary structure over time. If you need a per-residue

Re: [gmx-users] Zero Potential of Mean Force with g_wham

Thank you Jianguo. So can I use g_wham 4.5.2 even though I ran the simulations on 4.5.1? Best regards, Susana On Wed, Mar 9, 2011 at 2:31 PM, Jianguo Li ljg...@yahoo.com.sg wrote: I met the same problem when using 4.5.1 for some systems, the PMF shows zero curve, while the hist file looks

[gmx-users] Problem when running in many nodes

Dear all The last days I switched from Gromacs 3.3.3 to Gromacs 4.5.3, but I experience some difficulties when running in parallel. Initially, my simulation box has dimensions : * 3.30507 2.67145 41.15800* and it consists of 25 polymers chains with 50 beads/chain When I run NVT using 8 or

Re: [gmx-users] Problem when running in many nodes

Tomy van Batis wrote: Dear all The last days I switched from Gromacs 3.3.3 to Gromacs 4.5.3, but I experience some difficulties when running in parallel. Initially, my simulation box has dimensions : * 3.30507 2.67145 41.15800* and it consists of 25 polymers chains with 50 beads/chain

Re: [gmx-users] secondary structure propensities of residues

On 10/03/2011 1:36 AM, Justin A. Lemkul wrote: ZHAO Lina wrote: Hi, How do get the percentage of the secondary structure propensities of residues? seems dssp none such effect? The scout.xvg file contains everything you need (in a broad sense) - number of residues in a given secondary

Re: [gmx-users] Zero Potential of Mean Force with g_wham

On 10/03/2011 1:43 AM, Susana Tomasio wrote: Thank you Jianguo. So can I use g_wham 4.5.2 even though I ran the simulations on 4.5.1? Quite likely. Check the change logs on the GROMCACS website for relevant issues. Mark Best regards, Susana On Wed, Mar 9, 2011 at 2:31 PM, Jianguo Li

[gmx-users] surface tension in gmx

Dear gmx users, Since I am new to surface tension topic I need to ask very trivial questions. Please help me out with these simple questions. As a starting point I am going to calculate surface tension of a pure alkane in a cubic box and compare with experimental values. 1- g_energy is giving

Re: [gmx-users] Zero Potential of Mean Force with g_wham

Hi, I ran g_wham 4.5.2 and did get a non-zero PMF curve. I assume that there is something going on with g_wham on version 4.5.1. Thank you for your help. Susana On Wed, Mar 9, 2011 at 3:00 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 10/03/2011 1:43 AM, Susana Tomasio wrote: Thank

[gmx-users] heat capacity etc.

Hello, I want to calculate the isobaric heat capacity, the thermal expansion coefficient and the isothermal compressibility: i) My value for the heat capacity (NPT) is very low. I used option -nmol. Whan can be the reason or is the calculation of this property not accurate with this tool? By

Re: [gmx-users] heat capacity etc.

On 2011-03-09 19.48, Thomas Koller wrote: Hello, I want to calculate the isobaric heat capacity, the thermal expansion coefficient and the isothermal compressibility: i) My value for the heat capacity (NPT) is very low. I used option -nmol. Whan can be the reason or is the calculation of

Re: [gmx-users] surface tension in gmx

if you are interested in the surface tension of a pure liquid, which I assume is true from your message, then you need to create at least one surface, since periodic boundary conditions make the model system infinite, i.e., without a surface whatsoever. the easiest way to make that happen is to

[gmx-users] Treatment of protein termini when there are missing residues

Hello, My question concerns the 'best' way to treat the terminal groups for a protein that is missing residues at both termini, e.g. a 530 residue protein where only residues 15-512 are present in the pdb. My thoughts are that assigning charges to the end groups will result in areas of charge in

Re: [gmx-users] surface tension in gmx

Hi, 1- g_energy is giving #Surf*SurfTen by default. On the other hand surface tension can be obtained by gamma = (Pzz - (Pxx+Pyy)/2) / Lz. i.e Pres-XX-(bar), Pres-YY(bar), Pres--(bar) Can anyone tell me what the difference between these two is? They should be equal, bearing in mind units

Re: [gmx-users] Treatment of protein termini when there are missing residues

jo hanna wrote: Hello, My question concerns the 'best' way to treat the terminal groups for a protein that is missing residues at both termini, e.g. a 530 residue protein where only residues 15-512 are present in the pdb. My thoughts are that assigning charges to the end groups will

Re: [gmx-users] surface tension in gmx

regarding your first question, the definition of gamma is not correct, you are getting energy/length⁴ instead of energy/area (multiply by Lz instead of dividing by it) 2011/3/9 Pedro Alexandre de Araújo Gomes Lapido Loureiro palap...@gmail.com: Hi, 1- g_energy is giving #Surf*SurfTen by

Re: [gmx-users] heat capacity etc.

From g_energy -h: Some fluctuation-dependent properties can be calculated provided the correct energy terms are selected. The following properties will be computed: PropertyEnergy terms needed --- Heat capacity Cp

Re: [gmx-users] Treatment of protein termini when there are missing residues

On 10/03/11, Justin A. Lemkul jalem...@vt.edu wrote: jo hanna wrote: Hello, My question concerns the 'best' way to treat the terminal groups for a protein that is missing residues at both termini, e.g. a 530 residue protein where only residues 15-512 are present in the pdb. My

[gmx-users] RE: heat capacity etc.

-- NEU: FreePhone - kostenlos mobil telefonieren und surfen! Jetzt informieren: http://www.gmx.net/de/go/freephone -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] RE: heat capacity etc.

Hello, i) I use a NPT ensemble and the tool g_energy to extract the heat capacity. Nose-Hoover thermostat and Parrinello-Rahman barostat are used. Why do I get always c(V)? ii) When I use the tool g_energy -vis, I get the thermal compressibility, the adiabatic bulk modulus, but not the

[gmx-users] QMMM

Respected sir, I am new user in gromacs. I want to run QMMM on gromacs. Should I have install all source code like mopac7, guessin,gamess-UK for QMMM ? Please help me out. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

[gmx-users] spectral density calculation with GROMACS

Dear all, I am now developing a set of force field parameters and I want to calculate the spectral density with the normal mode analysis in GROMACS to check my parameters. The point here is that I want to get a plot (spectral density VS frequencies). Could anybody give me some slides or

[gmx-users] using one thermostat for entire system ??

I'm not sure what the reviewer has in mind. Therefore I would split the response into a number of possibilities. 1. If you simulated a box of those solute chemicals in the absence of a large solute, and if those solutes do not phase separate, then the collisions will equipartition the

[gmx-users] Zero Potential of Mean Force with g_wham

g_wham is not the only version of wham. Try using alan grossfield's version. Too often, I am afraid, gromacs accessory programs get broken in an update (not sure what the general solution is here beyond renewed calls for a proper test suite. Perhaps having 20+ programs is not ideal for a

[gmx-users] Re: gmx-users Digest, Vol 83, Issue 63

The choice for the QM package depends on what level of QM theory you wish to use and what package are available to you. to proceed sue the instructions http://wwwuser.gwdg.de/~ggroenh/qmmm.html Be aware though that QMMM is not to be considered a black box method. Gerrit 4. QMMM