[gmx-users] error in linking mopac and gromacs

According to the suggestion I have installed the f2c package in my machine.I am unable to find the g2c package. I have included the f2c library by - export LIBS="-lmopac -lf2c". But when I running  ./configure --with-qmmm-mopac --disable-float , an error is comming C compiler cannot create execu

RE: [gmx-users] git

Shouldn't you just do it anonymously? git clone git://git.gromacs.org/gromacs.git Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3

Re: [gmx-users] git

- Original Message - From: Sai Pooja Date: Friday, June 18, 2010 15:28 Subject: Re: [gmx-users] git To: Discussion list for GROMACS users > Thanks Justin. I installed git first and then used git clone > g...@git.gromacs.org:gromacs.git and this is what I get > Initialized empty Git re

Re: [gmx-users] git

Thanks Justin. I installed git first and then used git clone g...@git.gromacs.org:gromacs.git and this is what I get Initialized empty Git repository in /fs/home/sm868/gromacs/.git/ The authenticity of host 'git.gromacs.org (130.237.163.208)' can't be established. RSA key fingerprint is ef:9e:30:0

Re: [gmx-users] Enough hydration of the channel

Thanks a lot. On Fri, Jun 18, 2010 at 9:30 AM, Justin A. Lemkul wrote: > > > Aswathy wrote: > >> Thank you very much. >> >> In some papers I have seen the graph for hydration of the channel. How can >> we calculate that using Gromacs ? (or any other program?) >> > > Have a look at some of Oliver

Re: [gmx-users] Enough hydration of the channel

Aswathy wrote: Thank you very much. In some papers I have seen the graph for hydration of the channel. How can we calculate that using Gromacs ? (or any other program?) Have a look at some of Oliver Beckstein's programs: http://sbcb.bioch.ox.ac.uk/oliver/software/ There are several that m

Re: [gmx-users] Enough hydration of the channel

Thank you very much. In some papers I have seen the graph for hydration of the channel. How can we calculate that using Gromacs ? (or any other program?) Regards, -Aswathy On Thu, Jun 17, 2010 at 7:52 PM, wrote: > Determining how many waters is sufficient is a tough problem, try > successive

Re: [gmx-users] git

Sai Pooja wrote: Hi, This is the first time I am using git. I tried to get started by using - git clone git://git.gromacs.org/gromacs.git - command but got an error - "command not found: git" (I have tried different versions of this command available w

[gmx-users] git

Hi, This is the first time I am using git. I tried to get started by using - git clone git://git.gromacs.org/gromacs.git - command but got an error - "command not found: git" (I have tried different versions of this command available with the same result). I am sure this is something extremely tri

Re: [gmx-users] constraints bond length vari by 10%

- Original Message - From: Sebastian Waltz Date: Thursday, June 17, 2010 18:59 Subject: Re: [gmx-users] constraints bond length vari by 10% To: Discussion list for GROMACS users > Hi, > > I did read the Documentation 5 times now, but I still not > get is what the shake_tol does tell m

Re: [gmx-users] Incomplete ring

On 2010-06-17 21.06, you zou wrote: Hi Users, I have a .pdb file, in this file when I want to use pdb2gmx command there is this error massage: Fatal error: Incomplete ring in HIS680 this aminoacid is not complete in general, I don't know how can I complete this such that I don't add HIS for com

[gmx-users] Incomplete ring

Hi Users, I have a .pdb file, in this file when I want to use pdb2gmx command there is this error massage:Fatal error:Incomplete ring in HIS680 this aminoacid is not complete in general, I don't know how can I complete this such that I don't add HIS for complete? Please give me a hint. Thank you

Re: [gmx-users] [pairs] and [dihedrals]

you zou wrote: Hi everyone, I have one question about topology, If I want to write topology by hand, how can I write pairs and dihedrals without mistakes? Is there any free softwares to use? If you're using some automated program, then you're not doing it by hand :) There are several on

[gmx-users] [pairs] and [dihedrals]

Hi everyone, I have one question about topology, If I want to write topology by hand, how can I write pairs and dihedrals without mistakes? Is there any free softwares to use? Thank you _ Hot

Re: [gmx-users] large forces and monstrous water molecules in energy minimization step

Hi, For the dynamics to work you indeed need smaller forces (on the order of 10^3 in GMX units). Using flexible water molecules I was able to get this for your NaCl model. Just add: define = -DFLEXIBLE To your input. This should work also to fill in the voids I guess. Ran -- ---

[gmx-users] Enough hydration of the channel

Determining how many waters is sufficient is a tough problem, try successive runs of option #3, below. As for the simpler topic of getting more hydration: 1. If the issue is simply getting the channel hydrated enough to overcome some transition from dry to wet, then run a neat water box od

Re: [gmx-users] large forces and monstrous water molecules in energy minimization step

Use a different box size. I replicated your problem, but your run completes successfully with a box set up with editconf -d 1 instead of -d 3.3. If you set nstxout = 1 during the EM process, you'll see the problematic water molecule become unstable. It looks as if there is a small void in t

[gmx-users] RE: Parallel instalation: gmx-users Digest, Vol 74, Issue 76

Dear Carsten I give the path for the topol.tpr file now the error is change which is Fatal error: 3: Too many LINCS warnings (4254) 3: If you know what you are doing you can adjust the lincs warning threshold in your mdp file 3: or set the environment variable GMX_MAXCONSTRWARN to -1, 3: but no

[gmx-users] large forces and monstrous water molecules in energy minimization step

Dear GROMACS users, When trying to simulate a pair of interacting proteins in water, I have encountered problems that ultimately resulted in the simulation crashing. I then tried to simplify the system as far as possible while retaining the problem; I now believe the problem (or at least a part

[gmx-users] Enough hydration of the channel

Hi everyone, I have a homology model of a transporter. I want to study the ligand transport through the channel. i have done the following steps. 1. Ligand has docked to the mouth of the channel 2. Inserted the complex in POPC bilayer, then solvated, and equilibrated for 4ns(with position restar

[gmx-users] Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76

On Jun 17, 2010, at 3:42 PM, abdul wadood wrote: > Dear Carsten > > the command which i give is > > mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s topol.tpr > > with this command the same error come which is > > Can not open file: > 3: topol.tpr > 3: --

Re: [gmx-users] System net charge

Rabab Toubar wrote: I have noticed that you get the overall charge WHILE you are setting up the system - when using grompp I think. Now if after the mdrun and I want to check the overall charge, how can I possibly do that? I tried the mailing list but didn't find an answer to my question Th

[gmx-users] System net charge

I have noticed that you get the overall charge WHILE you are setting up the system - when using grompp I think. Now if after the mdrun and I want to check the overall charge, how can I possibly do that? I tried the mailing list but didn't find an answer to my question Thanks Rabab Toubar

Re: [gmx-users] Re: His protonation

Rabab Toubar wrote: So is there a way we can make His neutral before running the simulations as in case of NAMD? You can manually set any protonation state you want with pdb2gmx -his. -Justin Rabab Toubar --- On Wed, 6/16/10, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject:

Re: [gmx-users] Re: His protonation

So is there a way we can make His neutral before running the simulations as in case of NAMD? Rabab Toubar --- On Wed, 6/16/10, Justin A. Lemkul wrote: > From: Justin A. Lemkul > Subject: [gmx-users] Re: His protonation > To: "sagar barage" , "Gromacs Users' List" > > Date: Wednesday, June

[gmx-users] how to correct velocities in trajectory file

Dear gmx'ers, I've done a long NVE simulation in vacuo. During this run I had to take care to diminish the total energy drift, so my choice was comm_mode = None Now, analysing a smaller subsystem (solute + shell of solvent) I want to exclude its COM movement. Sorry, I fail to find any instruct

Re: [gmx-users] constraints bond length vari by 10%

Hi, I did read the Documentation 5 times now, but I still not get is what the shake_tol does tell me. I tried it with 10 values and can't figure out what it does. My CO bonds are constraint. Otherwise I would have bigger variations of the bond length. My .mdp file looks like this constraints

[gmx-users] calculate interfacial tension

Hello, I want to calculate the interfacial tension of the oil/water interface . I use 2D periodic boundary along Z axis , I get the interfacial teision from the .edr file (namely #Surf*SurfTen), it seems that the Surf*SurfTen is the total tension  of the two interface ,is it that ?  Does it has

Re: [gmx-users] Electric field, potential, dielectric constant

Hi, You may want to use a Poisson-Boltzmann solver, e.g., APBS for this purpose. Ran Vladimir Lankevich wrote: > Dear Gromacs Users, > > I have several questions about electrostatics in Gromacs. > I am simulating two proteins in water, separated by certain distance, > and was interested in their e

Re: Subject: [gmx-users] error compiling mopac and gromacs

According to the suggestion I have installed the f2c package in my machine.I am unable to find the g2c package. I have included the f2c library by - export LIBS="-lmopac -lf2c". But when I running  ./configure --with-qmmm-mopac --disable-float , an error is comming C compiler cannot create execu