[gmx-users] Freezing a portion of a protein during simulation

Hello Justin, Thanks a lot for your reply. I am using the option freezegrps in my .mdp file, given below: - ;define = -DSTRONG_POSRES define =

Re: [gmx-users] g_wham gets stuck

Amir Marcovitz wrote: Hi All, I have some problems with g_wham, and i already gone through all the postings and didn't find a hint.. basically, I'm trying to calculate PMF between two charged plates. I've performed a pulling simulation between the 2 plates according to Justin's UMBRELLA

[gmx-users] Re: pull distance

Dear Gromacs Users I have set my pull option as constant force and the pull geometry is distance the manual has stated that the pull_k1 unit is kJ/mol/nm . does it mean that the force applied to the protein is proportional to the distance between the 2 groups ? else what is it ? No, kJ/mol

Re: [gmx-users] angle

You could load your gro and trr file into vmd, label the angle, save the file and plot using excel. Oly On 28 April 2010 22:26, Justin A. Lemkul jalem...@vt.edu wrote: Nilesh Dhumal wrote: Hello, I am doing solvation of glucose. I am trying to calculate a angle between three selected

[gmx-users] comm-grps problem gromacs 4.0.4

Hi there, I'm running a 200ns simulation with a small trisaccharide in water. The trisacc drifts around the box. I've tried using comm-grps = System and comm-grps = blank and comm-grps = carb and what is below. carb is the name I use in my top file and index file. For the index I specify the

[gmx-users] Simulation of ONLY Lipid Bilayer

Hi all, I am using the pre-equilibriated layers from Tieleman. After the first energy minimization step, I removed the periodicity using trjconv. Now, in order to scale the lipid positions, I tried using Inflategro. Do I need to use strong position restraints (because that is for protein and I am

Re: [gmx-users] Simulation of ONLY Lipid Bilayer

On Thu, Apr 29, 2010 at 3:29 PM, Saumya samvygu...@gmail.com wrote: Hi all, I am using the pre-equilibriated layers from Tieleman. After the first energy minimization step, I removed the periodicity using trjconv. Now, in order to scale the lipid positions, I tried using Inflategro. Do I

[gmx-users] Freezing a portion of a protein during simulation

Hello Justin, Thanks a lot for your reply. I am using the option freezegrps in my .mdp file, given below: - ;define = -DSTRONG_POSRES define =

Re: [gmx-users] comm-grps problem gromacs 4.0.4

Oliver Grant wrote: Hi there, I'm running a 200ns simulation with a small trisaccharide in water. The trisacc drifts around the box. I've tried using comm-grps = System and comm-grps = blank and comm-grps = carb and what is below. Why wouldn't your trisaccharide diffuse around? The only

Re: [gmx-users] Freezing a portion of a protein during simulation

Anirban Ghosh wrote: Hello Justin, Thanks a lot for your reply. I am using the option freezegrps in my .mdp file, given below: - ;define =

[gmx-users] query about generation of 2D histogram

Respected Sir,     I am trying to generate free energy landscape by using g_sham,From the archive I came to know that one .xvg file needs to be prepared containing three columns of data, first one is time, 2nd and 3rd one are the coordinates of interest, I used the command g_sham -f *.xvg

Re: [gmx-users] comm-grps problem gromacs 4.0.4

Thanks for the help, With center of mass removal option I thought my sugar would stay in the center of the box. It does in the first simulation I ran however what I mean by diffuse is that it leaves the box on one side and enters from the other. There is nothing physically wrong with this but I'd

RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was

RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

Hi again, I thought your suggestions would work for my membrane, but it seems like the removal of COM translation of the bilayer and water separately does not stop the system from translating in the box. My new simulations are now soon crashing again since the lipids are crossing the pbc. I was

Re: [gmx-users] 64-bit gromacs-4.0.7 for Mac OSX

Hi, (...) Output from make: = (...) /bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno- unused -funroll-all-loops -L/usr/local/lib - framework Accelerate -o grompp grompp.o libgmxpreprocess.la ../mdlib/libmd.la

Re: [gmx-users] comm-grps problem gromacs 4.0.4

Oliver Grant wrote: Thanks for the help, With center of mass removal option I thought my sugar would stay in the center of the box. It does in the first simulation I ran however what I mean by diffuse is that it leaves the box on one side and enters from the other. There is nothing

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC because of spurious interactions with the other side of the membrane? That would certainly be a reason for a crash - the model physics is breaking down. How did you generate your initial

[gmx-users] Problem with Charmm in gromacs

Hi all, I have downloaded the latest git version of gromacs (yesterday) in which it is possible to use the charmm27 force field, I constructed the topology for my protein using the pdb2gmx program, everything goes ok also with the solvation, but then when i run the MD i notice that coulomb and LJ

Re: [gmx-users] Problem with Charmm in gromacs

Fabrizio Marinelli wrote: Hi all, I have downloaded the latest git version of gromacs (yesterday) in which it is possible to use the charmm27 force field, I constructed the topology for my protein using the pdb2gmx program, everything goes ok also with the solvation, but then when i run the MD

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

It is indeed not clear how you system may translate still! Is this translation on the z axis? How much does it move and how quick? On Apr 29, 2010, at 3:09 PM, Justin A. Lemkul wrote: Do you have sufficient water on either side of your membrane? That is, are the lipids crossing PBC

RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

My system consists of 128 lipids and 3655 water molecules and is one of the structures one can download from University of Calgary. I think that the water phase is thick enough because when I run non-constrained simulations and the system translates there is no crash when the lipids cross the

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

ERIKSSON, EMMA wrote: My system consists of 128 lipids and 3655 water molecules and is one of the structures one can download from University of Calgary. I think that the water phase is thick enough because when I run non-constrained simulations and the system translates there is no crash

Re: [gmx-users] g_wham gets stuck

Thanks for your answers, I tried to struggle a bit more with that today. my input dat files listings (i.e., tpr-files.dat, pullf-files.dat and pullx-files.dat) are fine and consistent with other in terms of file numbering. i use gromacs 4.0.5 on Linux with gcc 4.1.2 compiler. i run: *g_wham -it

RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

The last section of my mdp file: pull = constraint pull_geometry= cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DPPC pull_group1 = MOL pull_vec1= 0 0 1 pull_init1 = 3.083

Re: [gmx-users] 64-bit gromacs-4.0.7 for Mac OSX

- Original Message - From: J. Rui Rodrigues joaquim.rodrig...@estg.ipleiria.pt Date: Thursday, April 29, 2010 23:02 Subject: Re: [gmx-users] 64-bit gromacs-4.0.7 for Mac OSX To: Discussion list for GROMACS users gmx-users@gromacs.org Hi, (...) Output from make:

RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

The translation occurs in the z direction, yes. I'm running many constrained simulations but in general the movement of the new simulations, in which the COM translation has been removed for the bilayer and water separately, is about 1 nm in 3 ns. The movement is slower than when I was running

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

ERIKSSON, EMMA wrote: The last section of my mdp file: pull = constraint pull_geometry= cylinder pull_r1 = 1.0 pull_r0 = 1.5 pull_group0 = DPPC pull_group1 = MOL pull_vec1= 0 0 1 pull_init1

Re: [gmx-users] Problem with Charmm in gromacs

Fabrizio Marinelli wrote: Here it is my .mdp file, i attach you also the topology file, just to be more specific the one that are 0 are the SR interactions, thank you very much. For diagnostic purposes, can you re-process your structure using a different force field and try again? If the

RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

The increase in z box length is due to that I have replaced 12 DPPC lipids by cholesterol molecules. Cholesterol reduces the area per lipid and compresses the bilayer lateral (xy) area, resulting in a slight increase in the water layer thickness. I have performed exactly the same simulations

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

ERIKSSON, EMMA wrote: The increase in z box length is due to that I have replaced 12 DPPC lipids by cholesterol molecules. Cholesterol reduces the area per lipid and compresses the bilayer lateral (xy) area, resulting in a slight increase in the water layer thickness. I have performed exactly

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

Well 1 nm / 3 ns is definitely not reasonable! That is about 1 m / s ... 3.6 km/h We has seen motion of the COM of a bilayer using CG models but the motions were ~ 0.1 nm on the mircosecond timescale! This is due to the way COM is removed ... not exact but appears only on large time

RE: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

Justin, you understood it correctly; I only have problems with the low cholesterol concentration. According to g_traj -com the COM of DPPC in one of the simulations moves 0.6 nm in 3.5 ns. And as Xavier just wrote it's quite much... My mdp file looks like this: title=

[gmx-users] Hard Sphere?

Hello, I am not sure if anyone else has some experience with this, but I want to simulate a hard sphere in a solvent (water and heptane). I believe for the hard spheres, the attractive terms for LJ potential is very negligible so the only term to take into account is repulsion, from

[gmx-users] unstability of system, lincs problem

Dear Justin, Thank you for your answer. Regarding the message below: 1- How is it possible to have a reasonable max force but not a resonable potential? 2- To remove this high potential from system, What do you suggest? 2-1 Do I need to reduce the number of molecules in the box (reduce

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

ERIKSSON, EMMA wrote: Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p= 1.0 1.0e-14 compressibility = 4.5e-5 4.5e-15 I would bet almost anything that this is the cause of your problem. How did you come up with these

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

ERIKSSON, EMMA wrote: I was using those strange values of tau_p and compressibility to keep the z box length fixed in order to avoid problems associated with scaling the positions of the molecules in the box when we constrain the distance between DPPC and the small molecule. I was told to use

Re: [gmx-users] Constrained simulations crash when bilayer moves in the z direction in the box

Justin A. Lemkul wrote: ERIKSSON, EMMA wrote: I was using those strange values of tau_p and compressibility to keep the z box length fixed in order to avoid problems associated with scaling the positions of the molecules in the box when we constrain the distance between DPPC and the small

Re: [gmx-users] Problem with Charmm in gromacs

Hi Fabrizio, Could you send me the input files and I'll take a look at it. You can send it to bjelk...@cbr.su.se Regards, Pär Bjelkmar 29 apr 2010 kl. 16.34 skrev gmx-users-requ...@gromacs.org: Message: 3 Date: Thu, 29 Apr 2010 10:33:53 -0400 From: Justin A. Lemkul jalem...@vt.edu

[gmx-users] How to reduce high repulsion from system?

Dear experts, Could you please take a look at energy values. The system contains only stack of hexane molecules. MD sun gives lincs warning. 1- How can I get rid of high repulsive potential? *genconf_d -f Hexane.gro -nbox 4.0 8.0 8.0 -dist 1.1 0.55 0.55 -o Hexane-stack.gro*

[gmx-users] Units + normal mode analysis

Hello, I am doing normal mode analysis for my ststem. I run the following command. g_nmeig -f nm.mtx -s 2.tpr -of freq.xvg I could genrate the eigenfreq.xvg file. Can you tell what the units for wavenumber. It giving the unit [cm\S-1\N]. How can I convert to cm-1? Thanks Nilesh --

Re: [gmx-users] Units + normal mode analysis

Nilesh Dhumal wrote: Hello, I am doing normal mode analysis for my ststem. I run the following command. g_nmeig -f nm.mtx -s 2.tpr -of freq.xvg I could genrate the eigenfreq.xvg file. Can you tell what the units for wavenumber. It giving the unit [cm\S-1\N]. How can I convert to cm-1?

Re: [gmx-users] How to reduce high repulsion from system?

Here's an excellent learning experience. 1. Simplify the problem: minimize and attempt to equilibrate one single hexane molecule before trying to build your stacked structure. If the system blows up here, then the topology is likely to blame. More on this in a few moments. 2. Watch the

Re: [gmx-users] How to reduce high repulsion from system?

Justin A. Lemkul wrote: Here's an excellent learning experience. 1. Simplify the problem: minimize and attempt to equilibrate one single hexane molecule before trying to build your stacked structure. If the system blows up here, then the topology is likely to blame. More on this in a