[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 average

[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

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 sp...@xray.bmc.uu.sewrote: rams rams wrote

Re: [gmx-users] g_dipoles

of the orientation I suppose. Ram. On Tue, Mar 17, 2009 at 3:54 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: rams rams wrote: 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

[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

[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

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 sp...@xray.bmc.uu.sewrote: 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 description under

[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 list

[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

[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] 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

[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

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: rams rams

[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

[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

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 create a trajectory file from a set of pdb files (infact several

[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-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

[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 list

[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

Re: [gmx-users] S2 order parameters

: 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: D. van der Spoel and H.J.C. Berendsen: Molecular dynamics simulations of Leu

Re: [gmx-users] trjconv

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, I have a question about the option -fit in trjconv

[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.

[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

Re: [gmx-users] g_rotacf

, 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 these by integrating the output .xvg file of g_rotacf using g_analyze). Since the experimental values

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, I am so surprised for not finding any one who

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 am extremely sorry for incomplete information. But this is a follow

[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

[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

[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

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 the motion of backbone

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 Vitaly Chaban, Thanks

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 velocity autocorrelation function is 5.8*10^ -8

[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,

[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 list

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

[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

[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

[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

Re: [gmx-users] rot_diff

-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 generate the autocorrelation function of vectors (option -d). By defining vectors representing your

[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

Re: [gmx-users] segmentation fault

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 Justin and a few others who really helped me in successfully running insulin. Now, I am trying to setup the input file

[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

Re: [gmx-users] Re: warning mesgs

), 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 Gromacs installation is working properly (something I inquired about several days ago...) -Justin rams rams wrote: HI, When I use the merge command

Re: [gmx-users] Re: warning mesgs

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 very randomly thats why I could not keep update the things. Here I restarted every thing and have a look at and let

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 with pdb2gmx. Once you

[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 connectivities (i.e., values corresponding

[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 list

[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

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 segmentation error. Let me put the problem in a more elaborated way

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: Dear Tsjerk, Thanks

[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

[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 =

[gmx-users] trjconv - fit

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