[gmx-users] water medium

dear friends i want to simulate a water medium in which 5 types of different ions flow in it. how can i do that with gromacs? thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search bef

Re: [gmx-users] Computational Alanine Scanning

- Original Message - From: Binh Khanh Mai Date: Tuesday, May 18, 2010 14:10 Subject: [gmx-users] Computational Alanine Scanning To: gmx-users@gromacs.org --- | > > > Dear all, >     I'm trying use GROMACS to calculate bindi

[gmx-users] Computational Alanine Scanning

Dear all, I'm trying use GROMACS to calculate binding free energy with MM-PBSA method and do Computational Alanine Scanning. After run MD and obtain pdb files, I use PYMOL to mutate one residue to Alanine to estimate the energy difference between 2 structures. My issue is that I don't kn

RE: [gmx-users] g_sdf : error

Thanks. Its working. Why all coordinates are zero in refmol.gro file. NIlesh On Mon, May 17, 2010 9:31 pm, Dallas B. Warren wrote: > As I suspected: > > > Group16 ( C2) has 129 elements > Group17 ( C3) has 1 elements > Group18 ( C4) has 129 elements >

[gmx-users] Re: gmx-users Digest, Vol 73, Issue 98

Justin, Yes,it's fixed. Thank you. Zhang Cun > Message: 1 > Date: Mon, 17 May 2010 07:15:31 -0400 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] About wiki error > To: Discussion list for GROMACS users > Message-ID: <4bf12553.2070...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1

Re: [gmx-users] How to add an user-defined external potential

- Original Message - From: Sanku M Date: Tuesday, May 18, 2010 4:10 Subject: [gmx-users] How to add an user-defined external potential To: gmx-users@gromacs.org > Hi,>   I am planning to add an external harmonic potential along z direction > of a system : i.e U(z)= 0.5*K*z(**2)> I was wo

RE: [gmx-users] g_sdf : error

As I suspected: Group16 ( C2) has 129 elements Group17 ( C3) has 1 elements Group18 ( C4) has 129 elements As the error has told you, C3 does not have the same number of elements as C2 and C4. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition

RE: [gmx-users] g_sdf : error

Here are details. the first three groups from GUL residue and the last in cation (residue) Group 0 ( System) has 2584 elements Group 1 ( Protein) has 2456 elements Group 2 ( Protein-H) has 1036 elements Group 3 ( C-alpha) has 0 elements Group 4 (Backbo

RE: [gmx-users] g_sdf : error

Can you copy and paste into here what you see between: "Select a reference group and 1 group" And "Select a group:" When you run the script. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Par

RE: [gmx-users] g_sdf : error

hey Sorry for typing mistake. I used ths command. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt -r Nilesh On Mon, May 17, 2010 6:37 pm, Dallas B. Warren wrote: >> g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r > > Is that the exact command line you u

RE: [gmx-users] g_sdf : error

> g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r Is that the exact command line you used? If so, doubt it would actually work, since it should be: g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt -r Catch ya, Dr. Dallas Warren Drug Delivery, Dispositi

[gmx-users] g_sdf : error

Hello, I am trying to run g_sdf for sovlation for glucose in ionic liquids. I am trying to find distribution of anion around glucose. g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r First three group I selected from the same residue (Glucose). Forth grouup I selected from

[gmx-users] How to add an user-defined external potential

Hi, I am planning to add an external harmonic potential along z direction of a system : i.e U(z)= 0.5*K*z(**2) I was wondering if I can get an help on how to add an user-defined external potential like this in gromacs ? Thanks Sanku -- gmx-users mailing listgmx-users@gromacs.org h

Re: [gmx-users] OPLS-AA/L force field

you zou wrote: Dear Users, I have one question about Drug-Enzyme Complex,Similar to tutorial If I want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg Beta version" server too, or not? No. You can't use

[gmx-users] OPLS-AA/L force field

Dear Users, I have one question about Drug-Enzyme Complex,Similar to tutorial If I want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg Beta version" server too, or not?If I can't use this server, how can I mak

Re: [gmx-users] pressure for ambient water

On Mon, May 17, 2010 at 6:45 AM, Justin A. Lemkul wrote: > > > Amit Choubey wrote: > >> >> >> On Sun, May 16, 2010 at 7:41 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Amit Choubey wrote: >> >> >> >>On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul >>mailto:jalem

Re: [gmx-users] minimizing ligand only

Anna Marabotti wrote: Dear gmx-users, is it possible to minimize a ligand in vacuo, not inserted in a protein, using GROMACS? I tried to do it using the topology file created by PRODRG server and skipping the pdb2gmx, editconf, genbox steps, but GROMACS gave me an error indicating that it do

Re: [gmx-users] Gromacs test sets

Efrat Noy wrote: Hi everyone, I have just installed Gromacs (version 4.0.7), run the test sets (gmxtest-4.0.4) and got few failures. I looked at the relevant 'checkpot.out' and 'checkvir.out' files as suggested in previous messages. For the 'complex' tests I got no differences in the 'che

[gmx-users] minimizing ligand only

Dear gmx-users, is it possible to minimize a ligand in vacuo, not inserted in a protein, using GROMACS? I tried to do it using the topology file created by PRODRG server and skipping the pdb2gmx, editconf, genbox steps, but GROMACS gave me an error indicating that it does not recognize the molecule

[gmx-users] Gromacs test sets

Hi everyone, I have just installed Gromacs (version 4.0.7), run the test sets (gmxtest-4.0.4) and got few failures. I looked at the relevant 'checkpot.out' and 'checkvir.out' files as suggested in previous messages. For the 'complex' tests I got no differences in the 'checkpot.out', only in the

Re: [gmx-users] Total energy -decomposed terms

Moeed wrote: Dear Justin, Thanks so much for your comments. As for my question below: * ... Also, do LJ energy figures (or coulomb) given by g_energy refer to e11,e22.. interaction energies? Justin: By default, you will not get these interaction e

[gmx-users] Total energy -decomposed terms

Dear Justin, Thanks so much for your comments. As for my question below: * ... Also, do LJ energy figures (or coulomb) given by g_energy refer to e11,e22.. interaction energies? Justin: By default, you will not get these interaction energies decomposed

Re: [gmx-users] Domain decomposition error

Thanks Mark, I did play around with the -npme option a little and turns out using -npme 1 works for the system this is mdrun command I have in the script file mdrun_openmpi -nosum -dlb yes -npme 1 -cpt 40 -maxh 48 -deffnm md Thanks. Quoting Mark Abraham : - Original Message - From:

[gmx-users] Re: Need Help about GROMACS.

Regardless of whether or not you've received a response, please keep all correspondence on the gmx-users list. I am not a private tutor. To what post are you referring? The list is fairly high-traffic, so if it's been a long time since you posted, don't continue to wait for a response. Pos

Re: [gmx-users] pressure for ambient water

Amit Choubey wrote: On Sun, May 16, 2010 at 7:41 PM, Justin A. Lemkul > wrote: Amit Choubey wrote: On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul mailto:jalem...@vt.edu> >> wrote:

Re: [gmx-users] interaction parameter-polymer solution system

Moeed wrote: Dear experts, I am interested in calculation of Flory interaction parameter for ternary system of polyethylene/n-Hexane/ethylene. Flory-Huggins lattice theory for polymer solvent systems defines interaction parameter (binary) in terms of interaction energies between lattice s

[gmx-users] interaction parameter-polymer solution system

Dear experts, I am interested in calculation of Flory interaction parameter for ternary system of polyethylene/n-Hexane/ethylene. Flory-Huggins lattice theory for polymer solvent systems defines interaction parameter (binary) in terms of interaction energies between lattice sites. binary interac

Re: [gmx-users] About wiki error

Cun Zhang wrote: Hi, there seems two errors in the following page: http://www.gromacs.org/Documentation/Terminology/NVT say NVT is microcanonical ensemble. and http://www.gromacs.org/Documentation/Terminology/NVE say NVE is canonical ensemble. I register at wiki, but haven't authority to mo

Re: [gmx-users] PMF of ligand transport

Aswathy wrote: On Mon, May 17, 2010 at 12:14 PM, Aswathy > wrote: Hi, I tried to calculate PMF for the ligand transport using pull_geometry=position. Let me explain you what I did so far, I picked a small collection of backbone atoms nearly

[gmx-users] About wiki error

Hi, there seems two errors in the following page: http://www.gromacs.org/Documentation/Terminology/NVT say NVT is microcanonical ensemble. and http://www.gromacs.org/Documentation/Terminology/NVE say NVE is canonical ensemble. I register at wiki, but haven't authority to modify them. Can anybo

Re: [gmx-users] PMF of ligand transport

On Mon, May 17, 2010 at 12:14 PM, Aswathy wrote: > Hi, > > I tried to calculate PMF for the ligand transport using > pull_geometry=position. > > Let me explain you what I did so far, > > I picked a small collection of backbone atoms nearly from the centre of the > channel.My SMD was displacing th

Re: [gmx-users] ions

- Original Message - From: tahereh tekieh Date: Monday, May 17, 2010 18:01 Subject: Re: [gmx-users] ions To: Discussion list for GROMACS users > using second invocation of genion replaces new ions with the older ones if > the they have same amount of ions. That doesn't sound all that

RE: [gmx-users] RE: .rtp libraries lipids...

Hi, I am not exactly sure about your question, but for lipids and membrane composition there are several books about lipids e.g. The Lipid Handbook 'Biomembranes' by Gennis. A good source for topologies (itp-files) is: http://lipidbook.bioch.ox.ac.uk/ Best wishes Andreas > -Original Messa

Re: [gmx-users] RE: .rtp libraries lipids...

On 5/17/10 9:51 AM, lloyd riggs wrote: Dear All, This is a follow up on a post last week. I was trying to find pre-made .rtp libraries to add on for membrane lipids (other than DOPC, etc...). My critique was the complexity of membrane lipids means for most real processes we need to have a s

Re: [gmx-users] ions

using second invocation of genion replaces new ions with the older ones if the they have same amount of ions. On Mon, May 17, 2010 at 12:23 PM, Mark Abraham wrote: > > > - Original Message - > From: tahereh tekieh > Date: Monday, May 17, 2010 17:47 > Subject: [gmx-users] ions > To: gmx-u

Re: [gmx-users] ions

- Original Message - From: tahereh tekieh Date: Monday, May 17, 2010 17:47 Subject: [gmx-users] ions To: gmx-users@gromacs.org > hi gromacs users > how can i add multiple type of ions to my solvent. i tried it with genion but > it accepts only one type of ion. Add one lot of ions wit

[gmx-users] RE: .rtp libraries lipids...

Dear All, This is a follow up on a post last week. I was trying to find pre-made .rtp libraries to add on for membrane lipids (other than DOPC, etc...). My critique was the complexity of membrane lipids means for most real processes we need to have a synthetic membrane (s) that reflect real l

[gmx-users] ions

hi gromacs users how can i add multiple type of ions to my solvent. i tried it with genion but it accepts only one type of ion. thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search b