[gmx-users] GROMACS parameterization

Hello users, I have a question about the Gromacs parameterization. By using which water model (SPC / SPC/E / TIP3P etc) and their variants, the protein force field parameters in GROMACS were optimized ? Since a few of the properties of proteins depends upon the water models we employ (for instance,

[gmx-users] potential energy

Hi, I run a regular MD on a peptide with several conformations. I want to estimate the potential energy of each conformer. When I try using "g_energy" with the option of "Potential" using the corresponding ".edr" file, I am getting the average potential energy. But I am thinking that it is the aver

[gmx-users] creating a trajectory

Dear users, I extracted the pdb files from .trr and modified them according to my needs and I would like to convert the modified pdb files as a trajectory again to make use of gromacs tools. Is it possible in any means to do like that ? Thanks. ___ gmx-

[gmx-users] rot_correlation

Hi Xavier, I started working on the g_rms program (to obtain the rotation matrices) suggested by you as well as it was mentioned in a couple of papers for the calcualtion of rotational correlation times of proteins. Meanwhile, I have an idea like the following : The problem in using the MD gener

[gmx-users] least squares fit

Dear users, While doing the least squares fit, if I choose the "protein" as input group and "system" as output group, does it mean that the protein coordinates are rotated to give the best fit and the coordinates of the solvent and ions are modified with the same rotation matrices used for the pro

[gmx-users] trjcat

Dear Users, I tried to create a trajectory file from a set of pdb files (infact several of them) starting from time frame 0 to lets say 100 with an interval of 1ps each. If I use the following command, trjconv -f 0.xtc 1.xtc ..100.xtc -o .xtc its resuling only one frame (I think its not sti

Re: [gmx-users] trjcat

Dear Justin and Xavier, Thanks for the suggestions. Ram. On Tue, Oct 7, 2008 at 11:45 AM, Xavier Periole <[EMAIL PROTECTED]> wrote: > On Tue, 7 Oct 2008 11:39:45 -0400 > "rams rams" <[EMAIL PROTECTED]> wrote: > >> Dear Users, >> >> I tried to

[gmx-users] rot_correlation

Dear Xavier, I am sorry for posting an email which is not directly related to the gromacs. I have created a trajectory which contains the time dependent orientational changes of my reference structure (from the original trajectory generated by gromacs). I obtained the average rotational correalti

[gmx-users] trjcat

Dear users, I have nearly 2000 xtc files to concatenate. If I type them all at the command prompt (or by using a small script) they are stiched well. But, If I stich the first 1000 and the next 1000 separately and then if I try to stich these two together I could not stich them properlty. Is there

Re: [gmx-users] trjcat

Dear Justin, The following is the command I am using: trjcat -ffirst.xtc second.xtc -o total.xtc first.xtc and second.xtc are the stiched xtc files of first 1000 and second 1000 xtc files. Ram. On Mon, Oct 27, 2008 at 11:10 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: >

[gmx-users] hydrogen bond analysis

Dear Users, I have come across a few publications, where they have carried out the hydrogen bond analysis between the two substances. They reported the occupancy percentage of the two substances during the simulation. I really dont have any idea about these. What actually they corresponds to? Is t

[gmx-users] steered MD

Dear Users, Are there any online tutorials available to carry out the Steered molecular dynamics simulations using gromacs? If any one is familiar with it could you please share some information regarding the setting up the input files for SMD etc. Thanks in advance. Ram. ___

[gmx-users] steered MD

Dear users, I would like to carry out steered molecular dyanmics simulations on one of my protein dimer. I have a few questions to learn regarding this. 1. The mdrun program needs -pn index.ndx file The way I understand is, we need to create the index file with groups (say atom1 to which the spr

[gmx-users] smd_forces

Dear Users, Is there any criterion one should look for while defining the force (in absence of the experimental AFM studies) to pull the groups while performing the Steered Moleculear Dynamics simulations?? Thanks Ram. ___ gmx-users mailing listgmx-

[gmx-users] electric field effects

Dear users, Does any one aware of how to carry out the simulations in presence of a static and oscillating electric fields ? I found an option E_x, E_y, E_z needed to be mentioned in the run mdp file. Other than this are there any thing we need to mention ? Ram. __

[gmx-users] reg: simulations in presence of electric fields

Dear users, In the gmx manual it is mentioned that we can carry out the md simulations under electic fields (static I suppose). In the description under the title Electric Fields, it was described that number of cosines implemented is 1. What exactly it mean ?? The frequency is also 0. Does it mea

Re: [gmx-users] reg: simulations in presence of electric fields

Thank you very much David. Ram. On Sat, Jan 24, 2009 at 3:36 PM, David van der Spoel wrote: > rams rams wrote: > >> Dear users, >> In the gmx manual it is mentioned that we can carry out the md >> simulations under electic fields (static I suppose). In the descri

[gmx-users] g_dipoles

Dear Users, I am trying to obtain the dipole moment of a 40 amino acid residue peptide using g_dipoles. I am getting a huge number (about 700 Debye). I expect it to be around 150 Debye (based on other studies). To make sure it I extracted a shapshot of the structure and obtained the dipolemoment u

Re: [gmx-users] g_dipoles

Dear David, The peptide is having a -ve charge of 3. Though the components might dependent upon the orientation but the average might be the same irrespective of the orientation I suppose. Ram. On Tue, Mar 17, 2009 at 3:54 AM, David van der Spoel wrote: > rams rams wrote: > >>

Re: [gmx-users] g_dipoles

ents might > dependent upon the orientation but the average might be the same > irrespective of the orientation I suppose. > > Ram. > > On Tue, Mar 17, 2009 at 3:54 AM, David van der Spoel > wrote: > > rams rams wrote: > > Dear Users, > > I am trying to obtain the

[gmx-users] constraints

Dear Gromacs Users, I have a problem in running the energy minimization of a protein along with a substrate. In the .mdp file, if I use constraints = all-bonds, the system complains like the convergence is reached to system accuracy not to the one I mentioned. If I replace the constraints = none,

[gmx-users] disulphide bonds

Dear Gromacs users, Is there any way to handle the disulphide bond formed between two independent fragments of a protein ? Precisely it is an inter disulphide bond between two fragments. If I keep the two fragments as separate objects while preparing the pdb file (using TER between the two fragmen

Re: [gmx-users] disulphide bonds

to edit the topology file to remove the added hydrogen atoms ? Thanks Ram. On Thu, Jun 26, 2008 at 10:26 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > Hi Ram, > > Check the option -merge of pdb2gmx. > > Cheers, > > Tsjerk > > On Thu, Jun 26, 2008 at 6:11 AM,

Re: [gmx-users] disulphide bonds

me something to fix this ? Thanks and Regards, Ram. On Thu, Jun 26, 2008 at 3:34 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > rams rams wrote: > >> Dear Tsjerk, >> >> Thanks for the suggestion but when I use -merge command it says >> segmentati

Re: [gmx-users] disulphide bonds

Hi, If I use -ignh, that will ignore all the hydrogens in my input. And these hydrogens are added by the gromacs.in the first step of creating the top file. Ram. On Thu, Jun 26, 2008 at 3:34 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > rams rams wrote: > >> D

[gmx-users] insulin

Hi I am very new to Gromacs and I am really really running into problems while setting up the input file for insulin simulations. Are there any one who had bit experience in handling insulin (both the chains) ? ___ gmx-users mailing listgmx-use

[gmx-users] warning mesgs

Hi, I have three di sulphide bonds in my crystal structure. In the topology file it left blanks at the corresponding sulphur connectivities (i.e., values corresponding to gb_, ga_. gd_ ). When I try to create the .tpr file it complains the following: processing topology... Generated 716 of the 26

[gmx-users] Re: warning mesgs

without creating the peptide bond between the two chains ? On Fri, Jun 27, 2008 at 6:51 PM, rams rams <[EMAIL PROTECTED]> wrote: > Hi, > > I have three di sulphide bonds in my crystal structure. In the topology > file it left blanks at the corresponding sulphur connectiviti

Re: [gmx-users] Re: warning mesgs

: > > pdb2gmx -f (input).pdb -ignh -ter -merge > > I got the above to work perfectly on an insulin structure I found in the > RCSB (1ZNI), after deleting chains C and D from the .pdb file. If your > structure continues to give you headaches, try this one to make sure that > your G

Re: [gmx-users] Re: warning mesgs

mand you have written but with different output file) > > Nuno Azoia > > rams rams wrote: > >> Dear Justin, >> >> I am absolutely sorry for the discomfort. Since this is the first time I >> am using Gromacs, so things are not clear to me so I am trying things ve

Re: [gmx-users] Re: warning mesgs

is that fine if i change the SOL number in the top file created at the first step ? On Mon, Jun 30, 2008 at 1:50 PM, rams rams <[EMAIL PROTECTED]> wrote: > Here's where your problem is. This step is unnecessary! Once you have the > topology, there is no need to re-process wi

[gmx-users] segmentation fault

Dear users, Thanks a lot to Justin and a few others who really helped me in successfully running insulin. Now, I am trying to setup the input file for insulin with other enzyme and I am trying to merge the two chains of insulin. I am using the following command: pdb2gmx -f insu.pdb -p insu_p.top

Re: [gmx-users] segmentation fault

ol.top from Protein A. See Chapter 5 of the manual > for more details on this, but it is essentially analogous to including a > ligand topology (.itp) within a system topology (.top). > > -Justin > > rams rams wrote: > >> Dear users, >> >> Thanks a lot to Justi

[gmx-users] rot-diffusion

Dear users, Is it possible to evaluate the rotational diffusion of proteins using gromacs tools ?? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/s

[gmx-users] rot_diff

Dear users, Is it possible to evaluate the rotational diffusion of proteins using gromacs tools ?? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/s

Re: [gmx-users] rot_diff

On Sat, 5 Jul 2008 10:40:21 -0400 > "rams rams" <[EMAIL PROTECTED]> wrote: > >> Dear users, >> >> Is it possible to evaluate the rotational diffusion of proteins using >> gromacs tools ?? >> > No directly. However you can use g_rotacf to gene

[gmx-users] energy groups

Dear Users, I have a question about separating a system into energy groups. In my system, I have a metal atom and a few residues close to the metal atom (catalytic center). I ran the simulation with out any restraints. In the most representative structure, the catalytic center is completely distor

[gmx-users] energy groups

Dear Users, I have a question about separating a system into energy groups. In my system, I have a metal atom and a few residues close to the metal atom (catalytic center). I ran the simulation with out any restraints. In the most representative structure, the catalytic center is completely distor

[gmx-users] g_rotacf

Hi, I want to clarify a few of the things about the usage of g_rotacf (for rotational correlation function for molecules). In the manual it is given like the following: g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1 -fa expfit-x-P1 -beginfit 2.5 -endfit 20.0 I understood that -f, -s options

[gmx-users] g_rotacf

Hi, I am sorry if it is the second time I am posting the same thing. Two days back I have posted this but myself couldnt get a copy of the mail. So I am not very sure whether it reached the others member or not. I want to clarify a few of the things about the usage of g_rotacf (for rotational cor

[gmx-users] g_velacc

Dear Users, I am trying to calculate the velocity correlation functions to estimate the diffusion constant of my protein which is having nearly 50 residues. I am using the following command: g_velacc -f .trr -s .tpr -n .ndx -o .xvg -fitfn exp the output is the following: COR: COR: Correlation t

[gmx-users] Re: g_velacc

this. I also found a reasonably good value this time (in comparison to experiments for my diffusion constatns using g_msd). I want to make a comparison between the values obtained by einstein and Green-kubo relations. Thanks in advance. Ram. On Fri, Aug 29, 2008 at 5:32 PM, rams rams <[EM

Re: [gmx-users] Re: g_velacc

How to monitor the motion of center of mass of a protein as it is the case all the time to monitor this during the calculations of diffusion and correlation functions. How far the values will be different if we monitor the motion of backbone atoms rather than the center of mass motion. I still don

Re: [gmx-users] Re: g_velacc

, 2008 at 2:18 PM, rams rams <[EMAIL PROTECTED]> wrote: > How to monitor the motion of center of mass of a protein as it is the case > all the time to monitor this during the calculations of diffusion and > correlation functions. How far the values will be different if we monitor

Re: [gmx-users] Re: g_velacc

the diffusion constant as 1.9 * 10^ -8 A^2/ps^2 which is nothing but 1.9 * 10^ -4 m^2/s^2. But the time factor in mean square displacement should be in m^2 sec^-1. Did I missed any thing here ? Ram. On Mon, Sep 1, 2008 at 11:54 AM, rams rams <[EMAIL PROTECTED]> wrote: > Dear Vita

Re: [gmx-users] Re: g_velacc

Hi David Van der Spoel, You are right I missed the "dt" factor in the integral. Thanks a lot. Ram. On Mon, Sep 1, 2008 at 2:52 PM, David van der Spoel <[EMAIL PROTECTED]>wrote: > rams rams wrote: > >> Hi Vitaly Chaban, >> >> The calcualted value of vel

[gmx-users] reg:merging of files

Dear users, I have a general question regarding the merging of files: 1. If suppose I am rerunning a job, the new tpr file is created in the following way: tpbconv -s .tpr1 -f .trr1 -o .tpr2 Here, no confusion. The run with new tpr2 would give me .trr2 file. Now if I want to rerun again, tpbc

[gmx-users] COM monitoring

Dear users, Is it possible to monitor the center of mass motion of a protein using gromacs tools since this is the one to monitor in most of the dynamical studies of the protein. Thanks in advance. Ram. ___ gmx-users mailing listgmx-users@gromacs.o

[gmx-users] g_rotacf

Dear users, To calculate the rotational auto correlation functions, the command mentioned in the maual is: g_rotacf -P 1 -nparm 2 -fft -n index -o .xvg -fa -beginfit -endfit what are the -nparm and -fa options are meant for ? Also do we need to use -fitfn option to obtain the rotational auto c

[gmx-users] g_rotacf

Dear users, I have given a command like the following to calculate the rotational auto correlation function: g_rotacf -f .trr -s .tpr -P 2 -fft -o .xvg -b -e 1 -n .ndx -d I want to use the second order Legendre polynomial to fit. I integrated the resulting .xvg file, to obtain the cor

[gmx-users] g_rotacf

Hi, I am so surprised for not finding any one who have better experience with g_rotacf. I have been playing around with it and the time correlation value I got by g_rotacf is so small in comparison to the time correlation value I calcualted using the hydrodynamic radius of the protein. The value i

Re: [gmx-users] g_rotacf

corresponds to correlation time and in which units (its in ps I suppose) ? Thanks in advance. Ram. On Thu, Sep 4, 2008 at 2:32 AM, Xavier Periole <[EMAIL PROTECTED]> wrote: > On Wed, 3 Sep 2008 23:40:14 -0400 > "rams rams" <[EMAIL PROTECTED]> wrote: > >> Hi, &g

Re: [gmx-users] g_rotacf

the reasonable correlation time values with MD simulations. Ram. On Thu, Sep 4, 2008 at 11:02 AM, Xavier Periole <[EMAIL PROTECTED]> wrote: > On Thu, 4 Sep 2008 09:45:34 -0400 > "rams rams" <[EMAIL PROTECTED]> wrote: > >> Hi Xavier, >> >> I a

Re: [gmx-users] g_rotacf

EMAIL PROTECTED]> wrote: > On Thu, 4 Sep 2008 21:13:39 -0400 > "rams rams" <[EMAIL PROTECTED]> wrote: > >> Hi Xavier, >> >> I have a question about the accuracy of the correlation times obtained >> using >> gromacs tools. (I am getting the

[gmx-users] trjconv

Dear Users, I have a question about the option -fit in trjconv. The default option with -fit is none. If I use the option as rot+trans, does it mean that the rotational and translational motions are removed from the trajectory ? If not, is there any option in gromacs, to create a translational an

Re: [gmx-users] trjconv

ans performs an ordinary least-squares fit using the > reference structure provided with -s, removing rotational and > translational degrees of freedom. > > Cheers, > > Tsjerk > > On Tue, Sep 9, 2008 at 9:47 PM, rams rams <[EMAIL PROTECTED]> wrote: > > Dear Users,

[gmx-users] S2 order parameters

Dear users, The S2 order parameters obtained by using g_chi, are they corresponds to the Lipari_Szabo NMR order parameters for characterizing the internal motions? Also it is mentioned in the manual that the obtained S2 parameter corresponds to a dihedral and the generated plot is residue vs S2.

Re: [gmx-users] S2 order parameters

;wrote: > rams rams wrote: > >> Dear users, >> >> The S2 order parameters obtained by using g_chi, are they corresponds to >> the Lipari_Szabo NMR order parameters for characterizing the internal >> motions? >> > No, they are described here: > >

[gmx-users] correlation functions

Dear users, I am trying to obtain the rotational correlation times using gromacs tools. Though there are a couple of methods suggested by Xavier and others, I am trying to test it completely with gromacs tools. The basic idea is as suggested in the following article (also the article is suggested

[gmx-users] g_rotacf -normalize

Dear users, The default -normalize option in g_rotacf is set to yes. Does it mean that the vector of interest is always be a unit vector ? If so, this has to be set to -nonormalize I suppose if one is interested about the internal dynamics of a system. Please let me know whether I am correct or

[gmx-users] reg: vectors

Dear users, while calculating the correlation functions of a vector (using g_rotacf), are the vectors are normalized ? If not how can we obtain the correlation function with normalized vectors using gromacs tools ? ___ gmx-users mailing listgmx-users

[gmx-users] Re: reg: vectors

Hi, But if I want to look at the correlation function for an internal motion of a vector defined between two atoms, in that case whether the vectors are normalized or not are matter I suppose. Also, is it possible to monitor the dipolar correlation between two atoms of a protein ? Its always comp