[gmx-users] Liquid/Liquid

Hi all I want to simulate a biphasic system that I want to arrange the third types of molecules on the interface. would you please introduce to me a good tutorial? I can find a tutorial before but I lost it. Thanks alot Regards Maria -- gmx-users mailing listgmx-users@gromacs.org http://l

[gmx-users] RMS force is very large for shell MD

Dear gmx users: I have read a paper"Atomistic simulation of ion solvation in water explains surface preference of halides", I think it is a perfect work.  And I am also interested in the electrolyte  behavior at interface. I am using SWM4-NDP polarizable water model and ion Polarizable Alkali a

[gmx-users] regarding genbox

Dear all, I wanted to insert two different solute in a same solvent box. Can anybody suggest me how to do it. Thank you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/M

Re: [gmx-users] Liquid/Liquid

Maria Hamilton wrote: Hi all I want to simulate a biphasic system that I want to arrange the third types of molecules on the interface. would you please introduce to me a good tutorial? I can find a tutorial before but I lost it. Google is good at finding things :) Searching "Gromacs b

Re: [gmx-users] regarding genbox

Ravi Kumar Venkatraman wrote: Dear all, I wanted to insert two different solute in a same solvent box. Can anybody suggest me how to do it. Thank you. Assign positions to both solutes within the same box with editconf -box -center (to manually set the COM position rather than

Re: [gmx-users] regarding genbox

On 15/08/2011 9:22 PM, Justin A. Lemkul wrote: Ravi Kumar Venkatraman wrote: Dear all, I wanted to insert two different solute in a same solvent box. Can anybody suggest me how to do it. Thank you. Assign positions to both solutes within the same box with editconf -box -cente

Re: [gmx-users] negative dihedral cp (during cgenff conversion)

On 15/08/2011 10:50 AM, Peter C. Lai wrote: Random noob question: Should the cp field (field 7) in [ dihedraltypes ] always be positive or can it be negative? In the CGenFF conversion, the CHARMM dihedral has: OG302 CG2O2 CG321 CG331 -0.1500 1 180.00 ! LIPID methyl proprionate when I

[gmx-users] (no subject)

Hi all A very quick question. If I want to constrain all bonds in my system, is it just a case of setting constraints = all-bonds. Do I have to select the constraint algorithm. Here is my mpd file, I got no errors but its seems that this might be too simple. Note there is no relevance in the nam

[gmx-users] bond constraints

Hi all Sorry forgot to give a subject in the first e-mail. A very quick question. If I want to constrain all bonds in my system, is it just a case of setting constraints = all-bonds. Do I have to select the constraint algorithm. Here is my mdp file, I got no errors but its seems that this might b

Re: [gmx-users] bond constraints

Gavin Melaugh wrote: Hi all Sorry forgot to give a subject in the first e-mail. A very quick question. If I want to constrain all bonds in my system, is it just a case of setting constraints = all-bonds. Do I have to select the constraint algorithm. Here is my mdp file, I got no errors but it

[gmx-users] (no subject)

Hello, Using g_velacc I can calculate the velocity autocorrelation function of a group. Can I calculate the speed of a group instead of velocity ? I am using Gromacs 4.0.7 version. Thanks Nilesh vac.pdf Description: Adobe PDF document -- gmx-users mailing listgmx-users@gromacs.o

[gmx-users] Gromacs tool

Hi everyone, Any help will be appreciated, does gromacs have any tool to attach an alkyl chain or RGD to peptide -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Sear

Re: [gmx-users] Gromacs tool

Dina Kreter wrote: Hi everyone, Any help will be appreciated, does gromacs have any tool to attach an alkyl chain or RGD to peptide Gromacs does not have any molecule-building capacity. There are, of course, many other programs that do: http://www.gromacs.org/Documentation/File_Format

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

I am using the latest vesion of DSSP (the one available at DSSP homepage) 2011/8/11 Mark Abraham > On 10/08/2011 6:03 AM, César Ávila wrote: > > Hi, > I downloaded release-4-5-patches from git. It compiles and installs > successfully. Nevertheless I am getting a segmentation fault. > > > Are yo

[gmx-users] berendsen P coupling and fluctuation properties

Dear all, I noticed that applying Parrinello-Rahman (PR) pressure coupling even after equilibration with berendsen does not lead to target value for pressure when ;Bonds constraints = none is used. I tried Berendsen for to get fixed pressure ( 50 bar) but in the next run PR

[gmx-users] Velocity autocorrelation function

Hello, Using g_velacc I can calculate the velocity autocorrelation function of a group as a vector. Can I calculate the velocity autocorrelation function as a scalar? I am using Gromacs 4.0.7 version. Thanks Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.grom

[gmx-users] Hamiltonian replica exchange ?

Hi,    I was wondering whether hamiltonian replica exchange simulation has been implemented in latest version of  gromacs . Or, is there any other way of performing the hamiltonian replica exchange using some variants of lambda-dynamics ? Sanku-- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] berendsen P coupling and fluctuation properties

On 16/08/2011 7:05 AM, Elisabeth wrote: Dear all, I noticed that applying Parrinello-Rahman (PR) pressure coupling even after equilibration with berendsen does not lead to target value for pressure when ;Bonds constraints = none is used. The use of constraints and the

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

On 16/08/2011 7:04 AM, César Ávila wrote: I am using the latest vesion of DSSP (the one available at DSSP homepage) So, as discussed in some thread to which I was referring, there have been some changes to DSSP that prior versions of GROMACS don't cope with. Until GROMACS updates, use a versi