[gmx-users] Questions concerning autocorrealtion function

Hello! i)Here are the commands for my problem with the autocorrelation function which I mentioned in mails before: g_dist -f traj.trr -s topol.tpr -n index.ndx -o dist.xvg g_analyze -f dist.xvg -ac autocorr.xvg -P 2 Fatal error: Incompatible mode bits: normal and vector (or Legendre) What is

[gmx-users] specific heat

is there any command in gromacs that gives me a list of data points for specific heat and suseptibility as a function of temperature or time ? if not, then how can i calculate specific heat or polt Cv as a fuction of T? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/ma

Re: [gmx-users] specific heat

On 2011-01-30 11.43, leila separdar wrote: is there any command in gromacs that gives me a list of data points for specific heat and suseptibility as a function of temperature or time ? if not, then how can i calculate specific heat or polt Cv as a fuction of T? This is not trivial. You can com

[gmx-users] PME parameter in GROMACS

Dear all, I would like to know if there is a way in GROMACS to find or specify the value of kappa (or Ewald coupling/splitting parameter) for the PME technique that we use in our simulation. In my case, I would like to perform simulations with a specified kappa value and a grid size of A x A x A f

Re: [gmx-users] PME parameter in GROMACS

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 01/30/2011 01:18 PM, aldi asmadi wrote: > Dear all, > > I would like to know if there is a way in GROMACS to find or specify the > value of kappa (or Ewald coupling/splitting parameter) for the PME > technique that we use in our simulation. In my c

Re: [gmx-users] energy minimization of a charged system in vacuum

On 29/01/11 05:08, Matt Chan wrote: Perfect. This is great reading. Thanks for the pointers Mark. Matt On 01/28/2011 06:50 PM, Mark Abraham wrote: On 29/01/2011 9:57 AM, Matthew Chan wrote: Hi, I'm a first time GROMACS user. I've got 2 questions, which I'll ask in separate emails. The firs

Re: [gmx-users] energy minimization of a charged system in vacuum

On 2011-01-30 16.02, ms wrote: On 29/01/11 05:08, Matt Chan wrote: Perfect. This is great reading. Thanks for the pointers Mark. Matt On 01/28/2011 06:50 PM, Mark Abraham wrote: On 29/01/2011 9:57 AM, Matthew Chan wrote: Hi, I'm a first time GROMACS user. I've got 2 questions, which I'll

Re: [gmx-users] energy minimization of a charged system in vacuum

On 30/01/11 15:41, David van der Spoel wrote: My question is what effect does running a simulation with a charged system have? I recall reading that something related to PME calculations assumes the system is neutral, but it did not specify whether it was referring to MD or EM. From the mailing

Re: [gmx-users] energy minimization of a charged system in vacuum

On 2011-01-30 17.08, ms wrote: On 30/01/11 15:41, David van der Spoel wrote: My question is what effect does running a simulation with a charged system have? I recall reading that something related to PME calculations assumes the system is neutral, but it did not specify whether it was referrin

[gmx-users] ngmx doesnot work; CH3-CH2-OH

Hi Everyone, Program ngmx, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/tpxio.c, line: 1708 Fatal error: reading tpx file (md1.tpr) version 73 with version 58 program I installed 4.0.7 before, and now i installed 4.5.3. How can i use ngmx now? The second question is running C2H5OH

Re: [gmx-users] ngmx doesnot work; CH3-CH2-OH

gromacs wrote: Hi Everyone, Program ngmx, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/tpxio.c, line: 1708 Fatal error: reading tpx file (md1.tpr) version 73 with version 58 program I installed 4.0.7 before, and now i installed 4.5.3. How can i use ngmx now? You need a compati

Re: [gmx-users] ngmx doesnot work; CH3-CH2-OH

On 31/01/2011 11:15 AM, gromacs wrote: Hi Everyone, Program ngmx, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/tpxio.c, line: 1708 Fatal error: reading tpx file (md1.tpr) version 73 with version 58 program I installed 4.0.7 before, and now i installed 4.5.3. How can i use ngmx now?

Re: [gmx-users] ngmx doesnot work; CH3-CH2-OH

On 31/01/2011 11:34 AM, Justin A. Lemkul wrote: gromacs wrote: Hi Everyone, Program ngmx, VERSION 4.0.7 Source code file: ../../../../src/gmxlib/tpxio.c, line: 1708 Fatal error: reading tpx file (md1.tpr) version 73 with version 58 program I installed 4.0.7 before, and now i installed 4.5.3.

[gmx-users] luck

Hi everyone!   I have two questions.   1. after I installed gromacs 4.5.3 and "which mdrun" was able to give the correct path, I was not able to run "luck". Instead, "luck" gives an error "command not found". Is this ok? What went wrong? Do I need to install again gromacs?   2. I tried doing "pd

[gmx-users] Monitoring the water movement during simulation

Hi, I am completed a 3 ns simulation of a 230 aa protein .. Now I want to check whether the water is entering the proteins and through which side of the protein .. Since the whole protein is surrounded by water I don't know how this can be done .. is there any command to check .. also I have tried

Re: [gmx-users] solvation_box_preparation

Please tell me where I am wrong. I downloaded pdb of chaps and used prodrg server to get .itp and .gro file. Then I checked .itp for any missing charge and I found it correct. Then I created 6.0x6.0x6.0 box with genbox inserting 7 molecules of chaps.gro. Then again using genbox and -maxsol I put 51

Re: [gmx-users] luck

Mr Bernard Ramos wrote: Hi everyone! I have two questions. 1. after I installed gromacs 4.5.3 and "which mdrun" was able to give the correct path, I was not able to run "luck". Instead, "luck" gives an error "command not found". Is this ok? What went wrong? Do I need to install again gro

Re: [gmx-users] solvation_box_preparation

shahid nayeem wrote: Please tell me where I am wrong. I downloaded pdb of chaps and used prodrg server to get .itp and .gro file. Then I checked .itp for any missing charge and I found it correct. Then I created 6.0x6.0x6.0 box PRODRG doesn't have a problem of missing charges. It provides no

Re: [gmx-users] Monitoring the water movement during simulation

On 01/31/11, bharat gupta wrote: > Hi, > > I am completed a 3 ns simulation of a 230 aa protein .. Now I want to check > whether the water is entering the proteins and through which side of the > protein .. Since the whole protein is surrounded by water I don't know how > this can be done .

Re: [gmx-users] luck

Do I need to type in g_luck instead? --- On Mon, 1/31/11, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] luck To: "Discussion list for GROMACS users" Date: Monday, January 31, 2011, 12:11 PM Mr Bernard Ramos wrote: > Hi everyone! >  I have two questions. >  1. aft

Re: [gmx-users] luck

Mr Bernard Ramos wrote: Do I need to type in g_luck instead? Typing an email and waiting for a response takes far more time and effort than simply trying it yourself ;) -Justin --- On *Mon, 1/31/11, Justin A. Lemkul //* wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] l

Re: [gmx-users] luck

yup, i typed g_luck and it worked. the error that shows is   -- File input/output error: filename.pdb For more information, visit   --  --- On Mon, 1/31/11, Justin A. Lemkul

Re: [gmx-users] luck

Mr Bernard Ramos wrote: yup, i typed g_luck and it worked. the error that shows is -- File input/output error: filename.pdb For more information, visit -- Then "f

Re: [gmx-users] luck

thanks.     Here is the error i mentioned a while back with using pdb2gmx:   -- File input/output error: filename.pdb For more information, visit -- thanks for the time

Re: [gmx-users] Monitoring the water movement during simulation

I tracked the movement of water molecules around residues 65 to 67 of my protein (GFP crystal structure) .. According to the literature water should not enter the protein (reason being the cage like structure of GFP) .. but in VMD, 2 water molecules have been tracked to interact with chromophore ..

[gmx-users] 4.5.3 Installation under Cygwin

Hello, I am trying to install gromacs 4.5.3 on my desktop under Cygwin. Using the installation procedure from the Wiki: ( Install fftw-3.2.2 with ./configure --enable-sse --enable-float make make install Then install

Fwd: [gmx-users] Monitoring the water movement during simulation

-- Forwarded message -- From: bharat gupta Date: Sun, Jan 30, 2011 at 9:30 PM Subject: Re: [gmx-users] Monitoring the water movement during simulation To: Discussion list for GROMACS users I tracked the movement of water molecules around residues 65 to 67 of my protein (GFP crys

Re: [gmx-users] 4.5.3 Installation under Cygwin

On 01/31/11, toma0...@umn.edu wrote: > Hello, >     I am trying to install gromacs 4.5.3 on my desktop under Cygwin. Using > the installation procedure from the Wiki: > ( > Install fftw-3.2.2 with ./configure --enable-sse -

Re: Fwd: [gmx-users] Monitoring the water movement during simulation

On 01/31/11, bharat gupta wrote: > > > -- Forwarded message -- > From: bharat gupta > > Date: Sun, Jan 30, 2011 at 9:30 PM > Subject: Re: [gmx-users] Monitoring the water movement during simulation > To: Discussion list for GROMACS users > > > > I tracked the movement of

[gmx-users] Fwd: GROMACS user: error with pdb2gmx

I am not a free private GROMACS help service. Please direct correspondence to the users list. Please consider the advice here before doing so http://www.gromacs.org/Support Mark --- Begin Message --- Hi Mark!   Sorry to bother you. I am new to gromacs. I tried using pdb2gmx. However, after runn

Re: Fwd: [gmx-users] Monitoring the water movement during simulation

I followed the lysozyme tutorial step by step and everything seems to be fine and the literature cannot be wrong as it has been proved .. I have repeated this simulation second time... I want to ask one thing that during solvation step and equilibration step water is mixed with the protein so it me

Re: Fwd: [gmx-users] Monitoring the water movement during simulation

I followed the lysozyme tutorial step by step and everything seems to be fine and the literature cannot be wrong as it has been proved .. I have repeated this simulation second time... I want to ask one thing that during solvation step and equilibration step water is mixed with the protein so it me

Re: Fwd: [gmx-users] Monitoring the water movement during simulation

On 01/31/11, bharat gupta wrote: > I followed the lysozyme tutorial step by step and everything seems to be fine > and the literature cannot be wrong as it has been proved .. > Is your model of the chromophore reasonable? IIRC forming the chromophore requires making some new bonds. > I ha

Re: Fwd: [gmx-users] Monitoring the water movement during simulation

I selected the water molecules but using atom selection in VMD by using the following command "water and within 5 of resid 65 to 67", 65 to 67 is the chromophore position ... some 2 or 3 water molecules were found near to the chromophore i.e. inside the beta barrel ... Practically it should not ha