Re: [gmx-users] Constant Volume Simulation.

> Dear users, How can I do a constant volume simulation in Gromacs? By > removing Pressure coupling, it is constant pressure. No. Constant pressure is a bit of a misnomer - the algorithms used to achieve "constant pressure" simulations use feedback mechanisms to keep the pressure close to constant

Re: [gmx-users] mdrun output structure

> Final structure. > > On 6/30/06, Samuel C Flores <[EMAIL PROTECTED]> wrote: >> Hi Guys, >> >> Quick question: Is the output structure of mdrun designated by -c a >> final >> structure, or an average structure? I want the final structure -- am I >> better off extracting it from the .trr? It's a

Re: [gmx-users] Constant Volume Simulation.

+++ karamyog singh [Fri, Jun 30, 2006 at 03:27:47PM +0200]: > Dear users, How can I do a constant volume simulation in Gromacs? By > removing Pressure coupling, it is constant pressure. By removing both > Pressure and Temp coupling, it will be constant energy simulation. > What is the method of imp

[gmx-users] oplsaa force field

Dear GMX users, In ffoplsaanb.itp, there are 8 columns. ; name bond_typemasscharge ptype sigma epsilon opls_001 C 6 12.01100 0.500 A3.75000e-01 4.39320e-01 ; SIG In ffG53a5nb.itp, there are 7 columns. [ atomtypes ] ;name at.num mass charge

[gmx-users] g_sas

Dear all how can i compute solvent accessible surface area for a special residue in all of time? thanks __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___

Re: [gmx-users] mdrun output structure

Final structure. On 6/30/06, Samuel C Flores <[EMAIL PROTECTED]> wrote: Hi Guys, Quick question: Is the output structure of mdrun designated by -c a final structure, or an average structure? I want the final structure -- am I better off extracting it from the .trr? Sam -Original Message

[gmx-users] mdrun output structure

Hi Guys, Quick question: Is the output structure of mdrun designated by -c a final structure, or an average structure? I want the final structure -- am I better off extracting it from the .trr? Sam -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL

Re: [gmx-users] Van der Waals: switch attractive term off

It seems that you can modify the following line in the function *mk_nbfp() in force.c and achieve what you want. C6(nbfp,atnr,i,j) = idef->iparams[k].lj.c6; (it is in line 117 of force.c in version 3.3) and change it to C6(nbfp,atnr,i,j) = 0; This will set the attractive interaction

Re: [gmx-users] Scripting Analysis tools in tcsh

Hello GMX users, (this may be more of a tcsh question, but here goes anyway). I'm trying to write a script to go through some trajectories and calculate hbonding. It looks like this: #!/bin/tcsh foreach number (1 2 3 4 5 6 7 8 9 10 11) g_hbond -f ../../FullMD/FullMD$number.trr -s ../..

[gmx-users] Scripting Analysis tools in tcsh

Hello GMX users, (this may be more of a tcsh question, but here goes anyway). I'm trying to write a script to go through some trajectories and calculate hbonding. It looks like this: #!/bin/tcsh foreach number (1 2 3 4 5 6 7 8 9 10 11) g_hbond -f ../../FullMD/FullMD$number.trr -s ..

RE: [gmx-users] Temperature averages and log files

From: "Joanne Hanna" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Subject: [gmx-users] Temperature averages and log files Date: Tue, 27 Jun 2006 01:24:13 +0100 Hi I don't know if what I am going to ask has a very simple answer that I am missing but I am very confuse

[gmx-users] Constant Volume Simulation.

Dear users, How can I do a constant volume simulation in Gromacs? By removing Pressure coupling, it is constant pressure. By removing both Pressure and Temp coupling, it will be constant energy simulation. What is the method of implementing a constant volume simulation. Thanks. Karamyog Singh. Un

Re: [gmx-users] query about protein-ligand complex

On Fri, 2006-06-30 at 17:52 +0530, sangeeta wrote: > > Dear all, > > I am trying to run the dynamics of protein-ligand complex following the > tutorial "GROMACS Tutorial for Drug_Enzyme Complex version 3.3.1" > . I am running position restricted dynamics of the 91az8.pdb protein as > mentioned

[gmx-users] query about protein-ligand complex

Dear all, I am trying to run the dynamics of protein-ligand complex following the tutorial "GROMACS Tutorial for Drug_Enzyme Complex version 3.3.1" . I am running position restricted dynamics of the 91az8.pdb protein as mentioned in the tutorial trp.pdb & drg.pdb)in a Linux server machine, I c

RE: [gmx-users] Van der Waals: switch attractive term off

Title: RE: [gmx-users] Van der Waals: switch attractive term off I want to switch off LJ attractive to have my chains slip to each other and therefore increase the intanglements content. Suggestion? Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Instit

RE: [gmx-users] Van der Waals: switch attractive term off

From: "Alessandro Mattozzi" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Subject: [gmx-users] Van der Waals: switch attractive term off Date: Fri, 30 Jun 2006 10:14:28 +0200 Hi All I simulate PE using AUA. I would like to switch the attractive term of the vdW force.

[gmx-users] simple force field

dear gmx-users// I need a very simple force field to calculate very fast the internal energy of a given conformation of a small molecule. Since neither bond-lengths nor bond-angles will be varies, I think i only need terms for vdW, torsions and maybe electrostatics. It is also important to have

Re: [gmx-users] Van der Waals: switch attractive term off

Alessandro Mattozzi wrote: Hi All I simulate PE using AUA. I would like to switch the attractive term of the vdW force. How can I do it? By reading the relevant parts of the manual and working out how LJ terms are implemented and adjusting your topology and/or forcefield files accordingly.

[gmx-users] Van der Waals: switch attractive term off

Title: Van der Waals: switch attractive term off Hi All I simulate PE using AUA. I would like to switch the attractive term of the vdW force. How can I do it? Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Technology Royal Institute of Technology Stockholm, Swe