[gmx-users] RE : essential dynamics

Hi, After searching though gmxuserlist I found the relevant thread for ED... I followed the following steps :- 1) g_covar - to generate a covariance matrix and diagonalize it (for c-alpha atoms only) 2) g_anaeig - to generate eigen vectors 3)g_rmsf - for calculating RMSD of first 8 eigen vectors ,

[gmx-users] General MD question

Dear All, A quick question as I have not really delved into code for gromacs ever, nor know anyone close whom has worked on it. If I set up an MD simulation using a 4 protein complex, and 1 small peptide, plus waters, etc...and run the whole thing the proteins never move, only the amino acids

Re: [gmx-users] mdrun with append option

On 1/02/2011 7:50 AM, Sai Pooja wrote: I think I have figured out the reason. It is because I am carrying out replica exchange (manual) after every mdrun. If the exchange occurs, I exchange the checkpoint files, extend the simulation by 500 steps and continue. The new simulation starts from exc

Re: [gmx-users] Source Code for Lennard Jones Interaction

On 1/02/2011 9:04 AM, Apoorv Kalyankar wrote: Hello, I was wondering where can I find the source code for the Lennard Jones interaction (both simple cut-off and shifted cut-off) implemented in GROMACS 3.3. There is no single routine in that version or any other. Look at src/gmxlib/nonbonded/n

[gmx-users] extending a simulation

Dear gmx-users, In order to extend my simulations, i am using grompp in the following fashion: grompp -np 8 -t amphiphilic_512dppc_50ns -c amphiphilic_512dppc_50ns -e amphiphilic_512dppc_50ns -f 850ns.mdp -p dppc.top -o amphiphilic_512dppc_900ns followed by mdrun mpiexec -np 8 mdrun_mpi.o

Re: [gmx-users] General MD question

Hi Stephan, On Jan 31, 2011, at 5:18 PM, lloyd riggs wrote: > Dear All, > > A quick question as I have not really delved into code for gromacs ever, nor > know anyone close whom has worked on it. > > If I set up an MD simulation using a 4 protein complex, and 1 small peptide, > plus waters, e

Re: [gmx-users] Re: RE : essential dynamics

Hi Bharat, On Tue, Feb 1, 2011 at 8:33 AM, bharat gupta wrote: > Hi, > After searching though gmxuserlist I found the relevant thread for ED... I > followed the following steps :- What thread are you referring to? > 1) g_covar - to generate a covariance matrix and diagonalize it (for c-alpha >

Re: [gmx-users] 4.5.3 Installation under Cygwin

Thanks for the response. I tried building gromacs using cmake and the procedure from the wiki. Are there custom flags that I have to pass to cmake for it to work under cygwin? The cmake procedure seems to run fine without any errors, but I cannot evoke any gromacs tool following installatio

Re: [gmx-users] General MD question

Hi Stephan, It all a matter of time scale. Large molecules ==> slower movements (compare trucks and motor-bikes). Cheers, Itamar. On 1 February 2011 03:18, lloyd riggs wrote: > Dear All, > > A quick question as I have not really delved into code for gromacs ever, > nor know anyone close whom h

Re: [gmx-users] Re: RE : essential dynamics

Thanks for the reply ... I am following this thread - http://oldwww.gromacs.org/pipermail/gmx-users/2004-May/010438.html Also I read the following paper http://pubs.acs.org/doi/abs/10.1021/jp983120q (Internal dynamics of GFP) in w

[gmx-users] Charge groups

Dear All Suppose I determined partial charges on atoms of my molecules. How can I make charge groups of them? For example I have a drug of 50 atom(of course along with it's hidrogenes), and all of my data for charges are as 1.3465728 (suppose they are accurate and different to eachother) Is it p

[gmx-users] segmentation fault: g_velacc

Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time0.000 Segmentation fault When I do

Re: [gmx-users] hbond constraint

Denny Frost wrote: Since gromacs allows you to use quite a few different force fields with different naming schemes, how does it know (from reading the topology file) which atoms are hydrogens to enforce the hbond constraints? Atom types are present in [atoms], indicating what all of the

Re: [gmx-users] Charge groups

mohsen ramezanpour wrote: Dear All Suppose I determined partial charges on atoms of my molecules. How can I make charge groups of them? Look for similar groups in the force field you're using, and refer to the Gromacs manual, section 4.6.2. For example I have a drug of 50 atom(of course

Re: [gmx-users] segmentation fault: g_velacc

Vigneshwar Ramakrishnan wrote: Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time

Re: [gmx-users] segmentation fault: g_velacc

Hi, apparently this bug fix made it to 4.5, but not to 4.0. I will apply the fix also there. Carsten On Feb 1, 2011, at 1:58 PM, Justin A. Lemkul wrote: > > > Vigneshwar Ramakrishnan wrote: >> Dear All, >> I am using the gromacs 4.0.7 version and I was trying to calculate the >> momentum aut

Re: [gmx-users] extending a simulation

On 1/02/2011 8:27 PM, Adwait Mevada wrote: Dear gmx-users, In order to extend my simulations, i am using grompp in the following fashion: grompp -np 8 -t amphiphilic_512dppc_50ns -c amphiphilic_512dppc_50ns -e amphiphilic_512dppc_50ns -f 850ns.mdp -p dppc.top -o amphiphilic_512dppc_900ns

Re: [gmx-users] segmentation fault: g_velacc

Hi Vigneshwar, the problem is fixed now in the release-4-0-patches branch. Carsten On Feb 1, 2011, at 2:00 PM, Carsten Kutzner wrote: > Hi, > > apparently this bug fix made it to 4.5, but not to 4.0. > I will apply the fix also there. > > Carsten > > On Feb 1, 2011, at 1:58 PM, Justin A.

Re: [gmx-users] mdrun with append option

Thanks Mark. So if the simulation doesn't start from the checkpoint file, from where are the initial coordinates velocities etc. taken from?... the trajectory files? Also, I could not find the environment variable... and I am not sure how to use one. Pooja On Tue, Feb 1, 2011 at 3:03 AM, Mark Abr

Re: [gmx-users] mdrun with append option

>From the website: "If you change the integrator or ensemble, you should pass the checkpoint file to tpbconv only, not to mdrun, since the state might change and thus output files can not be appended." So now instead of supplying the checkpoint file to mdrun I supply it to tpbconv... does this as

Re: [gmx-users] mdrun with append option

Sai Pooja wrote: From the website: "If you change the integrator or ensemble, you should pass the checkpoint file to tpbconv only, not to mdrun, since the state might change and thus output files can not be appended." Are you changing the integrator, ensemble, and/or other settings? I

[gmx-users] g_velacc

Hello, I am trying to calculate the Velocity Autocorrelation Function for my system using g_velacc. I have system of 128 ionic liquids (128 cations and 128 anions). I run the trajectory for 20 ns. I used following command . g_velacc -f 3.trr -n emi-etso4-127-no.ndx -s 3.tpr -o I selected "syst

Re: [gmx-users] mdrun with append option

I am doing a manual replica exchange(generalized hamiltonian rem) after every mdrun. If the replica exchange is successful, then I "exchange checkpoint files". For example, consider the following: Simulation parameters:B1.B2 Replicas(coordinates and velocities):.R1.

[gmx-users] angle constrain, constrained PF6 anion

Dear all, I am setting up a simulation of ionic liquids with the PF6 anion. According to the potential, the anion should be kept rigid, wich obviously means that bond lengths and angles have to be constrained. LINCS doesn't work with angle constraints (i.e. constraing a triangle), so we

Re: [gmx-users] angle constrain, constrained PF6 anion

gyorgy.han...@fc.up.pt wrote: Dear all, I am setting up a simulation of ionic liquids with the PF6 anion. According to the potential, the anion should be kept rigid, wich obviously means that bond lengths and angles have to be constrained. LINCS doesn't work with angle constraints (i.e. co

Re: [gmx-users] mdrun with append option

Sai Pooja wrote: I am doing a manual replica exchange(generalized hamiltonian rem) after every mdrun. If the replica exchange is successful, then I "exchange checkpoint files". For example, consider the following: Simulation parameters:B1.B2 Replicas(coordinates

Re: [gmx-users] luck

Hi!   I am actually following your lysozyme tutorial. I ve been using different pdb files including that of water, methanol, 1AKI, etc. The pdb2gmx does not generate any topology file. No files are generated and I get this error:   -- pdb2gmx, VERSION 4.5.3

Re: [gmx-users] luck

Mr Bernard Ramos wrote: Hi! I am actually following your lysozyme tutorial. I ve been using different pdb files including that of water, methanol, 1AKI, etc. The pdb2gmx does not generate any topology file. No files are generated and I get this error:

Re: [gmx-users] luck

this is the command i am using:   pbd2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce then I choose a force fileld. then I get the error and no new files generated at all.   My working directory is: /cygdrive/c/MDProgram/Gromacs453/bin/molecule tests --- On Wed, 2/2/11, Justin A. Lemkul wrote:

Re: [gmx-users] luck

Mr Bernard Ramos wrote: this is the command i am using: pbd2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce then I choose a force fileld. then I get the error and no new files generated at all. My working directory is: /cygdrive/c/MDProgram/Gromacs453/bin/molecule tests I assume tha

Re: [gmx-users] angle constrain, constrained PF6 anion

The mdp file is attached. Best, Gyorgy Quoting "Justin A. Lemkul" : gyorgy.han...@fc.up.pt wrote: Dear all, I am setting up a simulation of ionic liquids with the PF6 anion. According to the potential, the anion should be kept rigid, wich obviously means that bond lengths and angles

[gmx-users] lactam bridge problems

I want to create a peptide bond between glu and lys using Gromacs 4.5.3. One option that I have is to modify the topology file (bonds, angles, etc.) but I also want to do a number of these lactam bridges so it is a pain to make the bonds, delete the atoms in glu and lys that are not needed and

Re: [gmx-users] luck

thanks. It was able to generate the needed files as indicated in the tutorial. I trnasfered my working directory.   many thanks.   Bernard --- On Wed, 2/2/11, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] luck To: "Gromacs Users' List" Date: Wednesday, February 2, 2

Re: [gmx-users] lactam bridge problems

Jerez Te wrote: I want to create a peptide bond between glu and lys using Gromacs 4.5.3. One option that I have is to modify the topology file (bonds, angles, etc.) but I also want to do a number of these lactam bridges so it is a pain to make the bonds, delete the atoms in glu

Re: [gmx-users] angle constrain, constrained PF6 anion

There's at least one problem that I see: dt = 0.0001 ! just to see if it starts This line won't be parsed properly. Check your mdout.mdp to see what grompp is assigning as a value for dt. You shouldn't need to set a value this small to see if it's going to work or

Re: [gmx-users] g_velacc

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 02/01/2011 05:49 PM, Nilesh Dhumal wrote: > Hello, > > > I am trying to calculate the Velocity Autocorrelation Function for my > system using g_velacc. I have system of 128 ionic liquids (128 cations and > 128 anions). I run the trajectory for 20

[gmx-users] Re: angle constrain, constrained PF6 anion

Hey Gyorgy, Your current topology file(s) is(are) also important to analyze the situation and fix the problem. Pass my kind regards to Julia... Dr. Vitaly V. Chaban, Ph.D. Department of Chemistry University of Rochester Rochester, New York 14627-0216 The United States o

Re: [gmx-users] Inaccurate pressure readings

Sorry to revisit this subject, but this output does not make sense. In the log file from my NPT simulation, the pressure readings fluctuate between about 300 bar and -300 bar, which I gather is pretty normal. However, at the end of the log file, it reports the average pressure being almost 1000 b

[gmx-users] Re: g_velacc

> I am trying to calculate the Velocity Autocorrelation Function for my > system using g_velacc. I have system of 128 ionic liquids (128 cations and > 128 anions). I run the trajectory for 20 ns.  I used following command > g_velacc -f 3.trr -n emi-etso4-127-no.ndx -s 3.tpr -o > > I selected "syste

Re: [gmx-users] lactam bridge problems

Justin, thanks a lot. I got the pdb2gmx to work now by changing the .hdb. I hope the simulation will be smooth sailing as well. Thanks, Jerez --- On Tue, 2/1/11, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] lactam bridge problems To: "Discussion list for GROMACS use

Re: [gmx-users] Inaccurate pressure readings

Denny Frost wrote: Sorry to revisit this subject, but this output does not make sense. In the log file from my NPT simulation, the pressure readings fluctuate between about 300 bar and -300 bar, which I gather is pretty normal. However, at the end of the log file, it reports the average pre

Re: [gmx-users] Inaccurate pressure readings

Here is the mdp file title = HEX cpp = /lib/cpp constraints = hbonds integrator = md dt = 0.002 ; ps ! nsteps = 250 ; total 5ns. nstcomm = 10 nstxout = 5 nstvout =

[gmx-users] Dynamics of non-protein molecules.

Dear All, I'm trying to use gromacs for molecular dynamics of surfactant micelles formation and dissolution. While reading User's manual and some beginners tutorials some questions and problems occur. 1. Is there some software for creating .pdb or .top file for non proteins molecules like

Re: [gmx-users] Inaccurate pressure readings

Denny Frost wrote: This is the 'averages' section " <=" = ### ==> " <=" === A V E R A G E S > " <=" = ### ==> " St" atistics over 1 001 steps u sing 1001 f rames Energies (kJ/mo l) Bond Angle Ry ckaert-Bell. LJ (SR) Coulomb (SR) 4.57E+03 3

Re: [gmx-users] Dynamics of non-protein molecules.

Yasen Atanasov wrote: Dear All, I'm trying to use gromacs for molecular dynamics of surfactant micelles formation and dissolution. While reading User's manual and some beginners tutorials some questions and problems occur. 1. Is there some software for creating .pdb or .top file for non

Re: [gmx-users] Inaccurate pressure readings

Sorry about that, I tried to delete that post because it was too long. The mdp file used to generate that data in the xvg file was the same except for the nsteps parameter. Also, I copied that file from excel where I was analyzing it and didn't realize until afterward that it had cut off the firs

Re: [gmx-users] Inaccurate pressure readings

Denny Frost wrote: Sorry about that, I tried to delete that post because it was too long. The mdp file used to generate that data in the xvg file was the same except for the nsteps parameter. Also, I copied that file from excel where I was analyzing it and didn't realize until afterward tha

[gmx-users] Protein in a solvated box

Hi, I have protein in a solvated box. When I used VMD to look at the system, I've found that the protein is not located at the center, but rather at the corner section. I would like to know why. Thanks for your insight in advance. Simon -- gmx-users mailing listgmx-users@gromacs

Re: [gmx-users] Protein in a solvated box

simon sham wrote: Hi, I have protein in a solvated box. When I used VMD to look at the system, I've found that the protein is not located at the center, but rather at the corner section. I would like to know why. FAQ #11: http://www.gromacs.org/Documentation/FAQs This should really be #

Re: [gmx-users] mdrun with append option

When I use .cpt file with tpbconv, I get the error pasted below. I checked the cpt file with gmxdump and it is not empty and has the same number of atoms. Reading toplogy and stuff from rex_1.tpr Reading file rex_1.tpr, VERSION 4.5.1 (single precision) NOTE: Reading the state from trajectory is an

Re: [gmx-users] mdrun with append option

Sai Pooja wrote: When I use .cpt file with tpbconv, I get the error pasted below. I checked the cpt file with gmxdump and it is not empty and has the same number of atoms. So use grompp, as I suggested before. Using gmxdump to verify the number of atoms is also not what I suggested; it c

Re: [gmx-users] mdrun with append option

On 2/02/2011 3:38 AM, Sai Pooja wrote: From the website: "If you change the integrator or ensemble, you should pass the checkpoint file to tpbconv only, not to mdrun, since the state might change and thus output files can not be appended." Where was that? It could use clarification. Mark So

Re: [gmx-users] mdrun with append option

Mark Abraham wrote: On 2/02/2011 3:38 AM, Sai Pooja wrote: From the website: "If you change the integrator or ensemble, you should pass the checkpoint file to tpbconv only, not to mdrun, since the state might change and thus output files can not be appended." Where was that? It could u

[gmx-users] RE : Essential dynamics

Hi, I have simulated (3ns) the crystal str of GFP (pdb -1GFL, without chromophore formation) and a modeled variant of GFP with a change in loop region (loop length is extended) . After calculating the RMSD of both strs. and superimposing reveals that RMSD doesnot fluctuate much for the modeled str

Re: [gmx-users] Re: RE : essential dynamics

I searched the user list in order to get some idea about calculating cosine content of first PCA .. but I am not able to do so ?? Can u direct me to a good thread or discussion.. On Tue, Feb 1, 2011 at 2:04 AM, bharat gupta wrote: > Thanks for the reply ... > > I am following this thread - > ht

Re: [gmx-users] segmentation fault: g_velacc

Thanks very much, Dr. Kutzner! On Tue, Feb 1, 2011 at 9:14 PM, Carsten Kutzner wrote: > Hi Vigneshwar, > > the problem is fixed now in the release-4-0-patches branch. > > Carsten > > > On Feb 1, 2011, at 2:00 PM, Carsten Kutzner wrote: > > > Hi, > > > > apparently this bug fix made it to 4.5, bu