Re: [gmx-users] Re: Gromacs 4.6 Installation under Cygwin

Hello, It looks like the problem might be in my mdp settings. I am using the MARTINI force field which uses shift functions for both electrostatics and vdw which are only available in the group-based cut-off scheme. OpenMP doesn't seem to run with the group-based cut-off scheme, just Verlet

Re: [gmx-users] Re: Gromacs 4.6 Installation under Cygwin

Hi, I have run the 3 scenarios that you mentioned. The commands and output are pasted below. Thanks, Mike ***Trial 1*** mdrun -v -deffnm Clp_Test -ntmpi 1 -ntomp 1 Reading file Clp_Test.tpr, VERSION 4.6 (single precision) Using 1 MPI thread Can not set thread affinities on the current pl

[gmx-users] Re: Gromacs 4.6 Installation under Cygwin

Hello, Thanks for the help. After setting the library path properly, I seem to be able to get gromacs up and running. However, I have run into another problem with mdrun and actually running any jobs. When I execute mdrun -v -deffnm Clp_Test -nt The output is: Reading file Clp_Test.tpr, V

[gmx-users] Gromacs 4.6 Installation under Cygwin

Hello, I am trying to install Gromacs 4.6 on a Windows workstation under cygwin. After I install everything, when executing g_luck I come up with the error: 'error while loading shared libraries: cyggmx-6.dll: cannot open shared object file: No such file or directory' There does exist t

Re: [gmx-users] 4.5.3 Installation under Cygwin

Thanks for the response. I tried building gromacs using cmake and the procedure from the wiki. Are there custom flags that I have to pass to cmake for it to work under cygwin? The cmake procedure seems to run fine without any errors, but I cannot evoke any gromacs tool following installatio

[gmx-users] 4.5.3 Installation under Cygwin

Hello, I am trying to install gromacs 4.5.3 on my desktop under Cygwin. Using the installation procedure from the Wiki: ( Install fftw-3.2.2 with ./configure --enable-sse --enable-float make make install Then install

Re: [gmx-users] g_clustsize output

Hello, Thanks for the response. g_clustsize outputs two xpm files of the weighted and non-weighted cluster size vs time. Is there another way for me to get number of clusters vs cluster size? Thanks, Mike On May 20 2010, David van der Spoel wrote: On 2010-05-20 04.55, toma0...@umn.edu

[gmx-users] g_clustsize output

Hello, I have a system of dimers which spontaneously assemble into clusters. I would like to get a plot of the number of clusters of size s vs s. In looking at g_clustsize I am able to obtain the average number of clusters vs time, the average cluster size vs time and a histogram of the ave

[gmx-users] pbc with nwall = 1

Hello, I want to study polymer adsorption onto a surface. To do so, I create a polymer-solvent system with a wall at z = 0 and use pbc = xy. This, however makes the system infinite in the z-direction. I was wondering if there was a way to create a periodic boundary at z = L such that when a

[gmx-users] Position restraints on a lipid bilayer

Hello, I am looking to add position restraints to some atoms of a lipid bilayer. There seem to be a lot in the list archives on this subject, but I am still a tad confused. What I would like to do is to position restrain the phosphorus atoms in only one leaflet of the bilayer. So how do I g

[gmx-users] Dextran Simulations

Hello, I would like to simulate the glucose polymer dextran (~5-10 subunits) and I am wondering what is the best way to do go about doing this. In looking at ffgmx.rtp I see GLCA/B which seem to be the glucose parameter files. If my numbering scheme is correct, to produce a linear dextran mo

[gmx-users] grompp not recognizing mdp file parameters

Hello, It seems that I am having a problem in that grompp is not recognizing the parameters that I enter into an mdp file, nor is it recognizing the text in the .top file. When I run a simulation, the output that I get is as follows: ERROR: invalid enum 'md' for variable integrator, using 'm

Re: [gmx-users] Applying a Uniform Shear

wrote: > toma0052 wrote: > > Hello, > > I am looking for a way in Gromacs that I could apply a uniform shear. > I > > have looked through the manual, and it seems that the methods for applying > > shear are using the cos_acceleration option or the deform option. The

[gmx-users] Applying a Uniform Shear

Hello, I am looking for a way in Gromacs that I could apply a uniform shear. I have looked through the manual, and it seems that the methods for applying shear are using the cos_acceleration option or the deform option. The deform option may work for me. However, I was reading in Allen and

[gmx-users] Pressure coupling and tau_p values

Hello, I am simulating a lipid bilayer system under a shear stress, in which I am interested in looking at the surface tension. I have done a number of simulations in an NPT ensemble using semiisotropic Berendsen pressure coupling. For a system such as this, I am wondering what would be an o

[gmx-users] g_msd and make_ndx

Hello, I am looking to measure the diffusion coefficient of a subset of water molecules moving through a pore in a lipid bilayer. In looking at g_msd and the -mol option, the manual states that my index file needs references to molecule numbers rather than atom numbers. I was wondering how I

Re: [gmx-users] Location of files under Cygwin

On 18 Apr 2007, Mark Abraham wrote: > toma0052 wrote: > > Hello, > > I am looking to edit a little bit of the source code in Gromacs, and I > > am having a little bit of a problem. Normally, I am using Gromacs that is > > installed on a network, but I cannot edit t

[gmx-users] Location of files under Cygwin

Hello, I am looking to edit a little bit of the source code in Gromacs, and I am having a little bit of a problem. Normally, I am using Gromacs that is installed on a network, but I cannot edit this, so I also have Gromacs installed on a personal windows machine running Cygwin. The installat

[gmx-users] Changing cos_acceleration

Hello, I am working with a DPPC lipid bilayer system in water, and I would like to add a shear force to the bilayer. Preferably, this force would be a function of the z coordinate and be maximal at the bilayer surface and decay to zero at the box top and bottom. For this, I have been looking

Re: [gmx-users] Deshuffling a .gro file

: > On 3/20/2007 10:03 PM, toma0052 wrote: > > Hello, > > I am performing a simulation in parallel on four processors. The > > simulation seems to run fine, and outputs a shuffled *.gro file. I would > > like to change the order of atoms to what they were in the or

Re: [gmx-users] grompp error with cpp

/cpp, but I am not sure why it is not working now. Should I just try to reinstall Gromacs? Thanks, Mike On 24 Mar 2007, David van der Spoel wrote: > toma0052 wrote: > > Hello, > > I just installed Gromacs on my windows machine under cygwin, and > > everything seeme

[gmx-users] grompp error with cpp

Hello, I just installed Gromacs on my windows machine under cygwin, and everything seemed to go fine with the installation and whatnot. Initially, when I tried to run a simulation, I obtained the error that Gromacs found the number of coordinates in my .top file to be 0, because it could not

[gmx-users] Deshuffling a .gro file

Hello, I am performing a simulation in parallel on four processors. The simulation seems to run fine, and outputs a shuffled *.gro file. I would like to change the order of atoms to what they were in the original input *.gro file, but I am having some trouble. I have seen some previous post

Re: [gmx-users] Frozen atoms and energy group exclusion

Hello, Thanks for the fast response. I went through my dppc.itp file and chose atoms such that the group of frozen atoms has a net charge of 0 as does the rest of the molecule. When running this through grompp, the error before about the atoms being in different charge groups is gone. Howev

[gmx-users] Frozen atoms and energy group exclusion

Hello, I asked a similar question to this a bit ago, but didn't get much of a response. I have a lipid bilayer system of 128 DPPC molecules in water. I want to fix the bottom face of the bilayer, and I am doing so by freezing the positions of the first 12 atoms of the DPPC molecule. The man

[gmx-users] Simulation in parts

Hello, I was wondering if I could run a simulation in parts. I would like to run a simulation for 100ps say, analyze it, and then sometime later continue on for another 100ps. It seems like all I would need to do is take the *.gro, *.trr, and *.edr files output from the first md simulation,

[gmx-users] Constant normal pressure simulation

Hello, I am looking to do a membrane simulation where I have a constant pressure normal to the membrane, and a fixed area of the membrane. Being semi-unfamiliar with pressure coupling schemes, how would I do this in Gromacs? It seems that even if I use the semiisotropic pressure coupling sch

[gmx-users] Pressure coupling question

Hello, I am simulating a lipid bilayer system, and am having some trouble understanding the pressure output. When I run a simulation, even when I do not add any perturbations or fix any atoms, the pressure oscillations are quite large. The temperature coupling seems fine. After about 1ps, t

[gmx-users] Help with energygrp_excl

Hello, I am doing some simulations on a DPPC bilayer that I got from Dr. Tieleman's website. I would like to examine shear forces necessary for membrane rupture. To do this, I have applied an acceleration to the head (First 12 atoms of each DPPC molecule, as numbered in the topology file) of

[gmx-users] Surface Tension of a lipid bilayer

Hello, I have a question about calculating the surface tension for the water-lipid interface of a lipid bilayer. After an MD run, I can use my .edr file and g_energy to calculate the surface tension. I believe that the surface tension is calculated something like gamma = (Pzz-(Pxx+Pyy)/2)/L.

Re: [gmx-users] indexing atoms *Altering code

2006, Mark Abraham wrote: > toma0052 wrote: > > Hello, > > I am wondering about a response I got a while ago about indexing > > atoms. I am not very familiar with awk, but it seems like a fairly simple > > way to search through a .gro file and find the solvent mole

Re: [gmx-users] indexing atoms

> /Erik > > On Tue, 2006-10-31 at 00:37 -0600, toma0052 wrote: > > Hello, > > I have a question regarding indexing atoms for use with > > non-equilibrium MD. The manual says that I can select atoms by number = > or > > type; I was wondering if there is a wa

[gmx-users] indexing atoms

Hello, I have a question regarding indexing atoms for use with non-equilibrium MD. The manual says that I can select atoms by number or type; I was wondering if there is a way in Gromacs to index atoms by position with the simulation box. I am looking to add an acceleration to the solvent, b

Re: [gmx-users] 1-4 Interactions

; Best, > > Tsjerk > > On 10/19/06, Mark Abraham <[EMAIL PROTECTED]> wrote: > > toma0052 wrote: > > > Hello, > > > I am starting simulations on a DPPC lipid bilayer taken from Peter > > > Tieleman's website. Upon trying to run the energy minim

[gmx-users] 1-4 Interactions

Hello, I am starting simulations on a DPPC lipid bilayer taken from Peter Tieleman's website. Upon trying to run the energy minimization, the program runs, but the results does not appear correct. During the run, I get the warning: Warning: 1-4 interaction between 908 and 913 at distance 1.

[gmx-users] p_4 error

Hello, I am running a simulation and when I attempt to use mdrun, I get the error p_4 error: interrupt SIGSEGV:11. I am not sure what this error is, but p_4 error apparently has something to do with shared programs. Also, strangly enough, when I type mdrun -h, I get the help information, but

[gmx-users] External Forces

Hello, I am simulating a DPPC lipid bi-layer, and I would like to add an external force to, for example, one layer of the bilayer. Do I add an external force by specifying groups and the acceleration on those groups in the mdp file? Is there another way to do this? Do I need to alter any ot

[gmx-users] Error with mdrun

Hi, I am trying to run a lipid bilayer simulation, and everything seems to be fine until I try to run mdrun. The simulation stops immediately after I begin mdrun, and I receive the error; p4_error: interrupt SIGSEV: 11. I am not really sure what this error is, nor what I should do to try to

[gmx-users] Lipid Bilayer Simulations

Hi, I am new to Gromacs, and I am working with lipid bilayer simulations. I am attempting to just run an energy minimization on a lipid bilayer so I can get a better feel for the program. I have taken the files dppc128.pdb, dppc.itp, lipid.itp and example2.itp from Peter Tieleman's website.

[gmx-users] Lipid simulations

Hello, I am just starting MD simulations of lipid bilayers using Gromacs. I am looking to add a force to a cetain set of atoms, one layer of a bilayer. I was wondering in anyone knew what program files I would need to modify in order to do this. Thanks, Mike Tomasini __

[gmx-users] Surface Tension Calculation

Hi, I posted a question a few days ago regarding the calculation of the surface tension of a lipid bilayer in Gromacs. The response that I got was to use the option "#Surf*SurfTens" in g_energy. I am not really sure how to do this. I have looked at the g-energy file in Gromacs, and I don't

[gmx-users] Gromacs Surface tension

Hi, I am not sure if this is how I should ask questions regarding Gromacs, but here goes. I was wondering if anyone knows if there is an internal program in Gromacs for calculating surface tension. I would like to model a lipid bilayer, and then determine the surface tension on that bilayer