[gmx-users] g_RMS: Mismatch of atom number between topology and reference structure

Hello, I am doing a refolding experiment, but I re-experience the same error. First of all, I use pdb2gmx for an input PDB structure, choose OPLS/AA force field and vacuum settings (no waters). Then I amke a box, and start simulations. What I want to do is to compare the starting unfolded

[gmx-users] RMSD truncation Restart simulation problems

Dear Gromacs Users/ Experts and Beginners, I'm using Gromacs 4.5.3 to run REMD simulation. The REMD simulations stooped abruptly and therefore the replicas have uneven information. One of the checkpoint differ in time and frame compared to other replicas. My case is very similar to the problem

Re: [gmx-users] .pdb file for DNA

Not really that Gromacs-related, but: In Ambertools, there's a program called nab(?) a.k.a. nucleic acid builder which performs that task very well. Sequence in, pdb-structure out, also for DNA single strands and RNA. Regards, Alex Dear All, I want to simulate interaction between single

Re: [gmx-users] Dihedral Restraints

The piece of code in dihres.c does it right (at least for the energy I would say... can't say anything about the force)... but the equation in the manual is wrong or at least misleading. On 05/03/11, Sai Pooja saipo...@gmail.com wrote: Hi,   In Manual 4.5.3, the potential for dihedral

[gmx-users] LINCS WARNING after good minimization and equilibration (NPT and NVT)

Dear GROMACS users, I only begin to work with gromacs and now have some problems with tetra protein. I used AMBER force field and made several changes (in ffamber.rtp, specbond.dat, ffamber99bon.itp) to create an isopeptide bonds between monomers. Minimization and equilibration (NPT and NVT) were

[gmx-users] Fw: How can I use trjorder ?

Dear all   I need to count the number of  H2 atom that is standing on the top of my sheet with distinct distance in my system . I 'd like use trjorder for it but don't know how can I use and after I make .xvg and .xtc file from trjorder command what should I do for numbering H2

[gmx-users] Support GTS 450

Hi, I would like to know. Are there any plans in the near future support for GROMAKS GTS450 ? -- Truly yours, Aleksei Medvedev http://aleks37.blogspot.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] g_RMS: Mismatch of atom number between topology and reference structure

Sergio Manzetti wrote: Hello, I am doing a refolding experiment, but I re-experience the same error. First of all, I use pdb2gmx for an input PDB structure, choose OPLS/AA force field and vacuum settings (no waters). Then I amke a box, and start simulations. What I want to do is to compare

Re: [gmx-users] .pdb file for DNA

You can try also 3DNA: http://rutchem.rutgers.edu/~xiangjun/3DNA/ Regards Paulo A. Netz On Mon, Mar 7, 2011 at 3:40 AM, majid hasan pu_majidha...@yahoo.com wrote: Dear All, I want to simulate interaction between single strand dna and cnt. I tried to use Biomer (from case group

[gmx-users] Dihedral angles distribution

Dear GMXusers I would like to obtain the normalized dihedral distribution of the alkyl chain of DPC molecules simulated with the CHARMM ff and GMX4.5.3. So i used the g_angle tool. I have constructed an index file which contain the 9 corresponding angles with make_index_mpi: a C12 | a C13 |

Re: [gmx-users] Dihedral angles distribution

sa wrote: Dear GMXusers I would like to obtain the normalized dihedral distribution of the alkyl chain of DPC molecules simulated with the CHARMM ff and GMX4.5.3. So i used the g_angle tool. I have constructed an index file which contain the 9 corresponding angles with make_index_mpi:

[gmx-users] Thermostat for equilibration

Dear users, Which temperature coupling scheme is recommended during equilibration? and do we have to use the same scheme for production MD also? Thanking you With Regards M. Kavyashree -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] LINCS WARNING after good minimization and equilibration (NPT and NVT)

zeppelin zeppelin wrote: Dear GROMACS users, I only begin to work with gromacs and now have some problems with tetra protein. I used AMBER force field and made several changes (in ffamber.rtp, specbond.dat, ffamber99bon.itp) to create an isopeptide bonds between monomers. Minimization and

Re: [gmx-users] Thermostat for equilibration

Kavyashree M wrote: Dear users, Which temperature coupling scheme is recommended during equilibration? and do we have to use the same scheme for Theoretically, any of them. Nose-Hoover does have a tendency to crash when dealing with systems that are far from equilibrium, though.

Re: [gmx-users] Thermostat for equilibration

Thank you sir for the reply! On Mon, Mar 7, 2011 at 5:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Dear users, Which temperature coupling scheme is recommended during equilibration? and do we have to use the same scheme for Theoretically, any of them.

Re: [gmx-users] questions regarding cutoff, charge groups, thermocouple and equlibration

On Sat, Mar 5, 2011 at 12:46 PM, Mark Abraham mark.abra...@anu.edu.auwrote: Assessing equilibration of an observable requires observing for a great deal longer than the time scale of the intrinsic variability of that observable. Only then can you assess whether any change in the value of

[gmx-users] Re: gmx-users Digest, Vol 83, Issue 40

Yes justin, the average is not 0 but around 0° (0.584577). But how to obtain the Average normalized dihedral distribution for example this dihedral? is few words the figure with g_angle ? http://cmt.dur.ac.uk/sjc/thesis_dlc/node106.html Thank you again sa wrote: Dear GMXusers I

Re: [gmx-users] Dihedral angles distribution

sa wrote: Yes justin, the average is not 0 but around 0° (0.584577). But how to obtain the Average normalized dihedral distribution for example this dihedral? is few words the figure with g_angle ? http://cmt.dur.ac.uk/sjc/thesis_dlc/node106.html The output you will get from

[gmx-users] membrane-protein tutorial

Dear all I am doing Membrane -protein tutorial. Actually I did each step carefully,I could score down my lipids 26 times. But there were two problems: 1-I get ~77 A for area per lipid in 26th step not 71 as Dr.Justin has said 2-I tried to do more iteration to make closer my area per lipid to

[gmx-users] select in pymol after trjconv

Hi, after added ions, I got a solv_ions.gro. I use trjconv to produce the solv_ions.pdb when I view it in pymol. I showed sequence, it like 1 2 3 4 6 ODOAOEOROHODOGOOYE But the solv_ions.pdb looks pretty regular. my problem is that, how could I choose the protein parts. I

[gmx-users] # Protein non-integer charge‏

Hi everybody, My problem is the following: I am studying the chromosome partitioning protein ParB from Burkholderia cenocepacia J2315. As no crystal structure was available, I used I-TASSER to predict its 3d structure. In order to refine the structure, I am now using in Gromacs the pdb file

Re: [gmx-users] membrane-protein tutorial

mohsen ramezanpour wrote: Dear all I am doing Membrane -protein tutorial. Actually I did each step carefully,I could score down my lipids 26 times. But there were two problems: 1-I get ~77 A for area per lipid in 26th step not 71 as Dr.Justin has said 2-I tried to do more iteration to make

Re: [gmx-users] # Protein non-integer charge‏

On 8/03/2011 1:11 AM, Marcelo Silva wrote: Hi everybody, My problem is the following: I am studying the chromosome partitioning protein ParB from Burkholderia cenocepacia J2315. As no crystal structure was available, I used I-TASSER to predict its 3d structure. In order to refine the

Re: [gmx-users] # Protein non-integer charge‏

Marcelo Silva wrote: Hi everybody, My problem is the following: I am studying the chromosome partitioning protein ParB from Burkholderia cenocepacia J2315. As no crystal structure was available, I used I-TASSER to predict its 3d structure. In order to refine the structure, I am now using

Re: [gmx-users] select in pymol after trjconv

On Mon, Mar 7, 2011 at 10:14 PM, Justin A. Lemkul jalem...@vt.edu wrote: ZHAO Lina wrote: Hi, after added ions, I got a solv_ions.gro. I use trjconv to produce the solv_ions.pdb when I view it in pymol. I showed sequence, it like 1 2 3 4 6 ODOAOEOROHODOGOOYE But

Re: [gmx-users] RMSD truncation Restart simulation problems

On 7/03/2011 8:23 PM, Henri Mone wrote: Dear Gromacs Users/ Experts and Beginners, I'm using Gromacs 4.5.3 to run REMD simulation. The REMD simulations stooped abruptly and therefore the replicas have uneven information. One of the checkpoint differ in time and frame compared to other replicas.

Re: [gmx-users] g_RMS: Mismatch of atom number between topology and reference structure

On 7/03/2011 7:33 PM, Sergio Manzetti wrote: Hello, I am doing a refolding experiment, but I re-experience the same error. First of all, I use pdb2gmx for an input PDB structure, choose OPLS/AA force field and vacuum settings (no waters). Then I amke a box, and start simulations. What I want

Re: [gmx-users] select in pymol after trjconv

ZHAO Lina wrote: On Mon, Mar 7, 2011 at 10:14 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: ZHAO Lina wrote: Hi, after added ions, I got a solv_ions.gro. I use trjconv to produce the solv_ions.pdb when I view it in

Re: [gmx-users] membrane-protein tutorial

Dear Dr.Justin Yes,I know,it deleted some lipids according to inflateGRO script in the first timethat I used perl command. Besides: I did iteration 25 times correctly,and no addition or doubling was occured. I used the same commands of 25th iteration.of course I changed numberes from 25 to 26 in

Re: [gmx-users] membrane-protein tutorial

mohsen ramezanpour wrote: Dear Dr.Justin Yes,I know,it deleted some lipids according to inflateGRO script in the first timethat I used perl command. Besides: I did iteration 25 times correctly,and no addition or doubling was occured. I used the same commands of 25th iteration.of course I

Re: [gmx-users] select in pymol after trjconv

ATOM397 N ALA48 35.480 52.940 57.920 1.00 0.00 ATOM398 H ALA48 34.740 52.570 57.360 1.00 0.00 ATOM399 CA ALA48 36.190 54.120 57.430 1.00 0.00 ATOM400 CB ALA48 35.900 55.320 58.350 1.00 0.00 ATOM401 C ALA48

[gmx-users] Tweeking MDP file options to run on GPU

Dear friends I am trying to run a ternary complex simulation using gromacs. so far the simulation is time taking on my dual-core maching 36hrs/ns. Fortunately or unfortunately I have a fermi graphics card wherein I can run the simulation quite fast. Now the unfortunate thing is

Re: [gmx-users] # Protein non-integer charge‏

Marcelo Silva wrote: Thank you Mark and Justin, I didn't specified the termini, but when I choose the zwitterionic forms the net charge becomes -4.670. You shouldn't; as I said before, zwitterionic termini are only for single amino acids, not full-length proteins. Without specifying

Re: [gmx-users] select in pymol after trjconv

ZHAO Lina wrote: ATOM397 N ALA48 35.480 52.940 57.920 1.00 0.00 ATOM398 H ALA48 34.740 52.570 57.360 1.00 0.00 ATOM399 CA ALA48 36.190 54.120 57.430 1.00 0.00 ATOM400 CB ALA48 35.900

Re: [gmx-users] select in pymol after trjconv

On Mon, Mar 7, 2011 at 10:45 PM, Justin A. Lemkul jalem...@vt.edu wrote: I'm guessing you have different chain identifiers, i.e. identical chains, just labeled A and B or something? I got four chains. and the .pdb from trjconv do not distinguish those things and don't show chain

Re: [gmx-users] membrane-protein tutorial

Dear Dr.justin Thank you.You are right. I did what you said. please let me know the answer of my other question in first email: I am doing iteration more than 26 times that you said in your tutorial. I am in 28th step now and my area per lipid is 63 and I think it is lowering everytimes I do

Re: [gmx-users] membrane-protein tutorial

mohsen ramezanpour wrote: Dear Dr.justin Thank you.You are right. I did what you said. please let me know the answer of my other question in first email: I am doing iteration more than 26 times that you said in your tutorial. I am in 28th step now and my area per lipid is 63 and I think it is

Re: [gmx-users] membrane-protein tutorial

Ok.Thank you very much On Mon, Mar 7, 2011 at 6:29 PM, Justin A. Lemkul jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Dr.justin Thank you.You are right. I did what you said. please let me know the answer of my other question in first email: I am doing iteration more than 26

[gmx-users] where does the gromacs looks for the top data file.

Hi, I got another question about where does the gromacs looks for the top data file. Specifically, The ~/bin ~/lib and ~/share are under my home directory. the general setting (in .bash_profile) can deal with executables (PATH) and libraries (LD_LIBRARY_PATH). How can I set up gromacs looking

[gmx-users] Re: gmx-users Digest, Vol 83, Issue 41

OK, i will try your suggestion. Thank you SA sa wrote: Yes justin, the average is not 0 but around 0° (0.584577). But how to obtain the Average normalized dihedral distribution for example this dihedral? is few words the figure with g_angle ?

Re: [gmx-users] where does the gromacs looks for the top data file.

ZHAO Lina wrote: Hi, I got another question about where does the gromacs looks for the top data file. Specifically, The ~/bin ~/lib and ~/share are under my home directory. the general setting (in .bash_profile) can deal with executables (PATH) and libraries (LD_LIBRARY_PATH). How can I

Re: [gmx-users] # Protein non-integer charge‏

Marcelo Silva wrote: The pdb command was: pdb2gmx -f prot.pdb -o prot_processed.gro -water spce There is a total of 297 residues. The pdb2gmx indicates that there are 4573 atoms but the topology file indicates 4577 atoms. It seems that is the arginine residue that is having problems:

[gmx-users] g_rmsf

Dear all, I want to calculate the C-alfa fluctuation of a protein during a trajectory with g_rmsf but I have just one question about the otput: which is the difference using -o output and -od output? So what is the difference between fluctuation and deviation? Thanks a lot in advance.

Re: [gmx-users] where does the gromacs looks for the top data file.

On Mon, Mar 7, 2011 at 11:11 PM, Justin A. Lemkul jalem...@vt.edu wrote: ZHAO Lina wrote: Hi, I got another question about where does the gromacs looks for the top data file. Specifically, The ~/bin ~/lib and ~/share are under my home directory. the general setting (in .bash_profile)

Re: [gmx-users] where does the gromacs looks for the top data file.

ZHAO Lina wrote: On Mon, Mar 7, 2011 at 11:11 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: ZHAO Lina wrote: Hi, I got another question about where does the gromacs looks for the top data file. Specifically, The ~/bin

Re: [gmx-users] g_rmsf

vferra...@units.it wrote: Dear all, I want to calculate the C-alfa fluctuation of a protein during a trajectory with g_rmsf but I have just one question about the otput: which is the difference using -o output and -od output? So what is the difference between fluctuation and deviation?

Re: [gmx-users] # Protein non-integer charge‏

Thank you Justin, that was exactly the problem. When I ran pdb2gmx in another computer it worked fine. I must have changed the .rtp file. Best regards, Marcelo Em 07-03-2011 15:14, Justin A. Lemkul escreveu: Marcelo Silva wrote: The pdb command was: pdb2gmx -f prot.pdb -o

[gmx-users] Membrane-protein tutorial

Dear Dr.Justin Is there any criteria for choosing vdwradii for carbon atoms? Because I have changed it from 0.15 to 0.375,but there were afew water molecules,it is difficult to delete them manually. then I decided to increase the vdwradii to 0.450 it is better now but i think the gap between

Re: [gmx-users] Membrane-protein tutorial

mohsen ramezanpour wrote: Dear Dr.Justin Is there any criteria for choosing vdwradii for carbon atoms? Because I have changed it from 0.15 to 0.375,but there were afew water molecules,it is difficult to delete them manually. then I decided to increase the vdwradii to 0.450 it is better now

Re: [gmx-users] g_rmsf

Thanks a lot. Valerio Justin A. Lemkul jalem...@vt.edu ha scritto: vferra...@units.it wrote: Dear all, I want to calculate the C-alfa fluctuation of a protein during a trajectory with g_rmsf but I have just one question about the otput: which is the difference using -o output and -od

[gmx-users] Instantaneous Square Displacement

Hi, I am writing a paper where I describe that gas molecules move inside a pore and then stick for long periods of time in occlusions in the pore wall. A reviewer has mentioned that I could illustrate this effect by using instantaneous square-displacement. I have already produced MSD

[gmx-users] using one thermostat for entire system ??

Hi, I simulated the diffusion of small gases (CO2, N2) in a framework structure which was mostly frozen with some mobile surface groups. I applied a temperature thermostat to the entire system (i.e I didn't couple the gas molecules and framework separately). I have now been asked the

[gmx-users] g_dipole

Hello, I am calculating vibrational spectra by calculating the Fourier transform of dipole moment correlation function. I have fortran code for the calculation of vibration spetra from the Fourier transform of dipole autocorrelation function. For better spectra I want to calculate the dipole

Re: [gmx-users] g_dipole

On 3/7/11 9:52 PM, Nilesh Dhumal wrote: Hello, I am calculating vibrational spectra by calculating the Fourier transform of dipole moment correlation function. I have fortran code for the calculation of vibration spetra from the Fourier transform of dipole autocorrelation function. For better

[gmx-users] Re-compile Gromacs Program?

Hi I found the Gromacs Program could not do the parallel computing since the staff of the compter center in my school upgraded the intel compiler to v 12, and rebuilt the mpich build with intel. I requested them to recompile the Gromacs Program but they rejected and they answered that the updated

[gmx-users] Disable non-bonded interactions between molecules

Dear all, I need to perform a simulation in which interactions between molecules (polymers) are calculated only via virtual sites. Within a molecule, non-bonded interactions between atoms should be present. Further, it would be best to be able to select which parts of the molecule

Re: [gmx-users] Re-compile Gromacs Program?

On 08/03/11, Chih-Ying Lin chihying2...@gmail.com wrote:     Hi I found the Gromacs Program could not do the parallel computing since the staff of the compter center in my school upgraded the intel compiler to v 12, and rebuilt the mpich build with intel. I requested them to

Re: [gmx-users] Disable non-bonded interactions between molecules

On 08/03/11, rue...@mpip-mainz.mpg.de wrote: Dear all, I need to perform a simulation in which interactions between molecules (polymers) are calculated only via virtual sites. Within a molecule, non-bonded interactions between atoms should be present. Further, it would be best to be

[gmx-users] Unsupported box diagonal

Hi, I am trying to do a simple membrane simulation of a h4 residue helix in DMPC. However, I encounter a strange issue this time when i try to run the final production run. the error that i get is as follows: Check for bad contacts and/or reduce the timestep. WARNING: Unsupported box diagonal

[gmx-users] QMMM

Hello everyone, I want install gromacs with mopac7 for qmmm. Can you guide me for installation procedure Thank you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] QMMM

On 8/03/2011 4:48 PM, Haresh wrote: Hello everyone, I want install gromacs with mopac7 for qmmm. Can you guide me for installation procedure There's a guide on the GROMACS webpage. Please search the web before asking questions :) Mark -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Unsupported box diagonal

On 8/03/2011 3:58 PM, Sweta Iyer wrote: Hi, I am trying to do a simple membrane simulation of a h4 residue helix in DMPC. However, I encounter a strange issue this time when i try to run the final production run. the error that i get is as follows: Looks like you haven't equilibrated well

Re: [gmx-users] using one thermostat for entire system ??

On 8/03/2011 2:50 AM, Jennifer Williams wrote: Hi, I simulated the diffusion of small gases (CO2, N2) in a framework structure which was mostly frozen with some mobile surface groups. I applied a temperature thermostat to the entire system (i.e I didn't couple the gas molecules and framework

Re: [gmx-users] Instantaneous Square Displacement

On 8/03/2011 3:01 AM, Jennifer Williams wrote: Hi, I am writing a paper where I describe that gas molecules move inside a pore and then stick for long periods of time in occlusions in the pore wall. A reviewer has mentioned that I could illustrate this effect by using instantaneous

[gmx-users] Generating toplogy

How to generate a toplogy file for a NMR pdb structure with Zn ions -- 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/Search before posting! Please don't post