[gmx-users] Re: MD with RMSD restraint

Hi, Position restraints do not allow me to do what I want. For instance, I want to allow the system to freely explore the conformational space within a certain RMSD range, but not evolve beyond a specified RMSD cutoff. Another application would be to push the system conformation away from the r

Re: [gmx-users] Re: MD with RMSD restraint

Sam Moors wrote: Hi, Position restraints do not allow me to do what I want. For instance, I want to allow the system to freely explore the conformational space within a certain RMSD range, but not evolve beyond a specified RMSD cutoff. Another application would be to push the system conformati

Re: [gmx-users] Re: MD with RMSD restraint

Another possibility is to patch gromacs with PLUMED http://merlino.mi.infn.it/~plumed/PLUMED/Home.html Here RMSD (and derivatives) is already implemented and you can easily restraint your MD simulation within a certain RMSD cutoff from a reference structure. Massimiliano On May 19, 2009, at

Re: [gmx-users] Re: MD with RMSD restraint

Hi, You can also use essential dynamics sampling. Ran. David van der Spoel wrote: > Sam Moors wrote: >> Hi, >> >> Position restraints do not allow me to do what I want. >> For instance, I want to allow the system to freely explore the >> conformational space within a certain RMSD range, but not ev

[gmx-users] .trr forces into VMD

Hi all I am looking for a way to import forces from a gromacs run into VMD for analysis. From a mdrun –rerun I have forces in a .trr file but VMD only reads the coordinates. Can you think of any way to get the forces into vmd instead of the coordinates? Thank you! Matteus

[gmx-users] Re: MD with RMSD restraint

Hi David, Thanks for your suggestion. However, I have a problem with the use of distance restraints in gromacs. As described in the manual a restraint potential is applied to each pair of atoms separately. Instead, I would like the restraint potential to depend on the root mean square of pair d

Re: [gmx-users] Re: MD with RMSD restraint

Hi, Sorry to pull a self-publicity plug, but you could use our MDDriver library [1] to implement whatever constraint you want as long as it can be calculated from the system positions and translates into forces to be applied to your system. Such a 'scripting' application is very briefly hinted

[gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex

Hello, I have a DNA-Zinc finger complex. What are the suitable forcefields for that type of complexes (the zinc ion is coordinated to 4 deprotonated cysteines)? I need to do some molecular minimization and dynamics including the nucelic acid sequence. Looking for some help. Thank you. Ne

[gmx-users] removal of water from hydrophobic core of lipid

Dear all I want remove water molecules from hydrophobic core of lipid by using script Keepbyz.pl by (chris neale) . I want to know basis of deciding uprez and lowrez variables . I mean to say how can I decide which value of uprez and lowrez is suitable for my system protein emb

Re: [gmx-users] removal of water from hydrophobic core of lipid

nitu sharma wrote: Dear all I want remove water molecules from hydrophobic core of lipid by using script Keepbyz.pl by (chris neale) . I want to know basis of deciding uprez and lowrez variables . I mean to say how can I decide which value of uprez and lowrez is suitable

Re: [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex

Nehme El Hachem wrote: Hello, I have a DNA-Zinc finger complex. What are the suitable forcefields for that type of complexes (the zinc ion is coordinated to 4 deprotonated cysteines)? The first step is probably to search in the literature for anything similar. Has anyone attempted such wo

Re: [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex

Hi, Have a look at http://wiki.gromacs.org/index.php/Parameterization and http://wiki.gromacs.org/index.php/Exotic_Species Next to that, also consider that you are talking about a site with -2 formal charge (ZnS4)2-. How likely is that? From QM studies, it seems much more likely that there are 1

[gmx-users] Selection of force field

Dear all, I want to study "glycolipid-protein" interaction using united atom GROMACS force field. For lipid simulation we need lipid.itp, which is a mixture of lipid ( Berger) and GROMOS (ffgmxnb) parameters.

Re: [gmx-users] .trr forces into VMD

Matteus Lindgren wrote: Hi all I am looking for a way to import forces from a gromacs run into VMD for analysis. From a mdrun –rerun I have forces in a .trr file but VMD only reads the coordinates. Can you think of any way to get the forces into vmd instead of the coordinates? If VMD wil

[gmx-users] Test suit failures

Dear gmx-users, I have done a test using test suit 4.0.4, and I got some failures as follows. All 16 simple tests PASSED FAILED. Check files in aminoacids FAILED. Check files in field FAILED. Check files in tip4p FAILED. Check files in water 4 out of 14 complex tests FAILED FAILED. Check files in

Re: [gmx-users] Test suit failures

Bert wrote: Dear gmx-users, I have done a test using test suit 4.0.4, and I got some failures as follows. All 16 simple tests PASSED FAILED. Check files in aminoacids FAILED. Check files in field FAILED. Check files in tip4p FAILED. Check files in water 4 out of 14 complex tests FAILED Chec

RE: [gmx-users] .trr forces into VMD

Hi, g_traj can write |f| or components of f in the b-factor field of a pdb file. I guess VMD can read and display that. I don't know if that will fulfill your needs. Berk > Date: Wed, 20 May 2009 00:19:59 +1000 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-user

[gmx-users] how to apply shear force

Hi all users, I am wondering how I can apply the shear force into the gromacs .Does anyone has such experoence about that? Really appreciate any suggestions. Yang ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listi

RE: [gmx-users] how to apply shear force

Hi, Read the pdf manual, it has an index entry for shear. Berk > From: yang...@mavs.uta.edu > To: gmx-users@gromacs.org > Date: Tue, 19 May 2009 15:10:24 + > Subject: [gmx-users] how to apply shear force > > Hi all users, > > I am wondering how I can apply the shear force into the gromacs

[gmx-users] FudgeQQ parameter with TraPPE FF and OPLS-AA

Dear GMX-users. I'm trying to do free energy calculations for calculations of partitions coefficients. My normal defaults section of TraPPE topologies are: ; nbfunc    comb-rule   gen-pairs   fudgeLJ fudgeQQ       1            3               no          0.5 

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

sovent accesible surface area? On Mon, May 18, 2009 at 11:09 AM, Tsjerk Wassenaar wrote: > stretching != swelling, e.g. > > On Mon, May 18, 2009 at 10:46 AM, Bhanu wrote: > > How about checking radius of gyration??? > > > > 2009/5/18 Tsjerk Wassenaar > >> > >> Hi, > >> > >> Well, I think 'swell

[gmx-users] gromacs on glacier.westgrid.ca

Hi All, Is there anyone who is running gromacs on glacier.westgrid.ca machine? If yes, I will be appreciated if he/she can tell me how to run gmx on this facility. I either get error messages which says either the executable or the topology file can not be found. Regards, Payman _

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

Well, why didn't I think of that? Maybe because flattening will also increase the SAS, or (partial) unfolding, or opening of two domains... :) Tsjerk On Tue, May 19, 2009 at 6:10 PM, Marius Retegan wrote: > sovent accesible surface area? > > On Mon, May 18, 2009 at 11:09 AM, Tsjerk Wassenaar >

Re: [gmx-users] shift function for vdwtype and density

Dear David: Thank you so much for the valuable information. "Our conclusion in the above paper is to use PME for Coulomb and not shift Van der Waals" I have read the paper you mentioned and did not find how you treated the VdW. Have you done some work on the cut off method for vdw? Since I used

Re: [gmx-users] Selection of force field

Hi Anindita, Proper carbohydrate parameters were introduced in G45a3. But you're not easily satisfied, wanting proteins carbohydrates and lipids to work together! You're short of wanting to include nucleic acids :) Anyway, the lipids are a bit problematic. There are parameters for some lipids for

Re: [gmx-users] Re: MD with RMSD restraint

Sam Moors wrote: Hi David, Thanks for your suggestion. However, I have a problem with the use of distance restraints in gromacs. As described in the manual a restraint potential is applied to each pair of atoms separately. Instead, I would like the restraint potential to depend on the root me

Re: [gmx-users] gromacs on glacier.westgrid.ca

Hi Payman, That is probably not the only grid facility on which Gromacs may be run and it would be helpful if you could give specifications of it (WMS software e.g.), which could give you more response. Also, it would be helpful if you'd be able to give more information regarding the output. Then

RE: [gmx-users] gromacs on glacier.westgrid.ca

Dear Tsjerk, Thanks for your e-mail. The message that cluster sends is: "Running on 4 processors. Starting run at: Sat May 16 17:13:28 PDT 2009 Warning: Command line arguments for program should be given after the program name. Assuming that ./global/home/pirzadeh/gromacs-4.0.4/bin/mdrun_d is a c

Re: [gmx-users] gromacs on glacier.westgrid.ca

Payman Pirzadeh wrote: Dear Tsjerk, Thanks for your e-mail. The message that cluster sends is: "Running on 4 processors. Starting run at: Sat May 16 17:13:28 PDT 2009 Warning: Command line arguments for program should be given after the program name. Assuming that ./global/home/pirzadeh/groma

Re: [gmx-users] shift function for vdwtype and density

Dear all: This is the mdp I just used for the system. The funny thing is after a 8ns simulation I got a very high pressure and temperature: Temperature 343.437 Pressure (bar) 45.782 I also did another run with removing the vdw_switch in mdp and keep all other conditi

RE: [gmx-users] gromacs on glacier.westgrid.ca

Hi Justin, Following is the script I use. But remember several points: 1. I compiled the gmx with double precision and did not rename the code to mpi. I kept whatever was produced with _d suffix. 2. I use the same script for other codes and they work (I am using other MD code for special purposes a

Re: [gmx-users] gromacs on glacier.westgrid.ca

Payman Pirzadeh wrote: Hi Justin, Following is the script I use. But remember several points: 1. I compiled the gmx with double precision and did not rename the code to mpi. I kept whatever was produced with _d suffix. "Whatever was produced" does not inspire confidence. You're sure that --

[gmx-users] dt > = 0.002

Hi I want to get the simulation results fater and want to set the time step dt > = 0.002 what is the upper limit of the time step dt ? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-user

Re: [gmx-users] dt > = 0.002

Chih-Ying Lin wrote: Hi I want to get the simulation results fater and want to set the time step dt > = 0.002 what is the upper limit of the time step dt ? Some textbook reading is probably in order here. Also of interest are papers describing constraint algorithms. Ultimately the t

Re: [gmx-users] dt > = 0.002

Hi Lin, I would suggest taking a look at the manual, specifically section 6.5 (Removing Fastest Degrees of Freedom), and any general textbook on molecular simulation. Wanting faster results without having an understanding of the method is a good recipe for getting the wrong answer. There

[gmx-users] g_clustsize method

I am planning on using g_clustsize to do some condensation analysis. I looked at g_cluster and see that it has a number of method options including single linkage and jarvis patrick. Is it true that g_clustsize has only the single linkage option? I took a look at the source code but this type

Re: [gmx-users] shift function for vdwtype and density

Yanmei Song wrote: Dear all: This is the mdp I just used for the system. The funny thing is after a 8ns simulation I got a very high pressure and temperature: Temperature 343.437 Pressure (bar) 45.782 I also did another run with removing the vdw_switch in mdp

RE: [gmx-users] mdp file for local pressure

Is there a local pressure version of Gromacs 4? I can only find Gromacs version 3.02 with local pressure. If there is, could you tell me where to get it? Thanks. Daniel From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf O

Re: [gmx-users] g_clustsize method

Jacob Spooner wrote: I am planning on using g_clustsize to do some condensation analysis. I looked at g_cluster and see that it has a number of method options including single linkage and jarvis patrick. Is it true that g_clustsize has only the single linkage option? I took a look at the sou

[gmx-users] Selection of force fields

Dear Tsjerk,    Thanks for your reply. I am interested to work with ganglioside GM1. In that case which ffG will be appropriate for me. Ms. Anindita Gayen  C/O Dr. Chaitali Mukhopadhyay  Senior Research Fellow  Department of Chemistry  University of Calcutta  92, A. P. C. Road

Re: [gmx-users] Selection of force fields

Hi Anindita, I was sort of afraid you might be dealing with glycosphingolipids. The Gromos force fields do not have properly behaving models for sphingolipids yet. I'm not sure whether other force fields do much better. There's some serious parameterization to do here. If you have experimenal data