[gmx-users] data points missing

Dear users, In one of the simulations I have run, I have transfered it from one system to another so some data points were missing what I should do now. how to find which data points are missing? Thank you With regards M. Kavyashree -- gmx-users mailing listgmx-users@gromacs.org http://li

[gmx-users] AFM Simulation

Hi everyone. I'm doing a simulation of a system where a peptide is linked to a surface and an AFM tip is brought in contact to do force measurements. The AFM tip moves very slowly (1nm/ms), so I'm simulating stationary tips at various distances. Does anyone know the most direct measurement f

Re: [gmx-users] MD - analysis

Dear Sir, g_mindist analysis showed the violation of minimum image convention, it was violated over a short period of time and then it came back to normal. I attach the plot herewith. Should this data be discarded or any useful information can be obtained. Thank you With Regards M. Kavyashree

Re: [gmx-users] Water Potential Energy

On 14/06/2011 4:18 AM, Rini Gupta wrote: Dear gmx-users, I am using GROMACS 4.5.4 to run a pure water system using SPC/E model containing 32000 molecules. I have done the equilibration for 2 ns followed by production run of 5 ns using NPT ensemble at 300K. I am using PME for treating electrost

[gmx-users] rdf

Hello, I have a system with 128 emi (cations) and 128 Cl (anions). I want to study is there any bifurcated interaction between hydrogen of cation and CL atoms or CL atom interacting with 2 different hydrogen of cation. For this I considered all CL atoms are distinguishable. I am thinking to run

[gmx-users] Re: nonormalize option in g_rotacf

Hi Justin, Thanks so much. I really appreciate your time looking into this. Like you said, it is hard to imagine that this could possibly be a bug. Anyway, I will submit an issue in a few days if there are no other comments. Andrew -- Date: Sun, 12 Jun 2011 20:43:39 -0400 From

[gmx-users] Gradually increasing the force constant during restrained MD runs

Dear Aditi: you can do this by scripting gromacs to run in short segments, modifying the force constant for each run. e.g.: #!/bin/bash for((i=1;i<=100; i++)); do let "j=i-1" grompp -f ${i}.mdp -p ${i}.top -f ${j}.gro -o ${i}.tpr mdrun -deffnm ${i} done You only need to use some more s

[gmx-users] Water Potential Energy

Dear gmx-users, I am using GROMACS 4.5.4 to run a pure water system using SPC/E model containing 32000 molecules. I have done the equilibration for 2 ns followed by production run of 5 ns using NPT ensemble at 300K. I am using PME for treating electrostatic interactions (cut-off 0.9 nm). My quest

Re: [gmx-users] helix dihedral constraint

Sanku M wrote: Hi, I wanted to run an atomistic simulation where I would like to constrain helicity of a helical peptide( i.e the initial configuration is an ideal helix) . I was wondering whether there is a way to constrain the helix dihedral angles in Gromacs. Also, if there is any other

[gmx-users] helix dihedral constraint

Hi, I wanted to run an atomistic simulation where I would like to constrain helicity of a helical peptide( i.e the initial configuration is an ideal helix) . I was wondering whether there is a way to constrain the helix dihedral angles in Gromacs. Also, if there is any other option to keep the

Re: [gmx-users] Regarding H-bond autocorrelation

Hi, The problem is that g_hbond subtracts a "background level" to compensate for the finite size of the system. I thought that feature had been taken away, however. Are you using old code? Erik 12 jun 2011 kl. 19.33 skrev bipin singh: > Hello, > > I am calculating the H-bond autocorrelation

[gmx-users] Gradually increasing the force constant during restrained MD runs

Hello All! I am running an MD simulation on RNA with orientation restraints. Instead of using a single force constant for the whole trajectory, I want to start with a very low force constant and increase it gradually and regularly up to a final suitably high value and then continue the simulati

Re: [gmx-users] ionic strength and PME

vidhya sankar wrote: Dear justin, Thank you for your previous reply. When i study the effect of ionic strength on stability Which Parameter of Electrostatics Should i use? . If I use usual PME Then will it interfere it with result?. Because My system has

[gmx-users] ionic strength and PME

Dear justin,   Thank you for your previous reply.   When i study the effect of ionic strength on stability Which Parameter of Electrostatics Should  i use? . If I use usual PME  Then will it interfere it with  result?. Because My system has Non zero charge  I went t

Re: [gmx-users] gromacs 2.1

You can try also $ git tag release-1-6 release-1-6-01 release-2-0 release-2-0-01 release-2-0-02 release-3-0 release-3-1 release-3-1-1 release-3-1-2 release-3-1-3 release-3-1-4 release-3-2 v4.0.7 v4.5 v4.5-beta1 v4.5-beta2 v4.5-beta3 v4.5-beta4 v4.5.1 v4.5.2 v4.5.3 v4.5.4 # git checkout release-2

Re: [gmx-users] Re: Force field parameters for phosphorylated

sarah k wrote: Dear Bharat, You can use the Dundee PRODRG server to prepare the topology/parameter of any structure for GROMACS or some other programs. Here is the link: Be careful with PRODRG, its results are not good (posted for the second time in 15 minutes): http://www.gromacs.org/Do

[gmx-users] Re: Force field parameters for phosphorylated

Dear Bharat, You can use the Dundee PRODRG server to prepare the topology/parameter of any structure for GROMACS or some other programs. Here is the link: http://davapc1.bioch.dundee.ac.uk/prodrg/ you should tag the phosphate group and draw the structure of phosphotyrosine and load it. Good Luck

Re: [gmx-users] Reducing density using -vdwd option for a new solvent in the system

shivangi nangia wrote: Hello dear gmx-users, I am trying to create a system which has 2,5-dihydobenzoic acid (DHB) as the solvent ( with a positively charged protein and few DHB anions) in a box. I have created the .itp and .gro file of DHB using PRODRG. Unrelated advice - the topology

[gmx-users] Reducing density using -vdwd option for a new solvent in the system

Hello dear gmx-users, I am trying to create a system which has 2,5-dihydobenzoic acid (DHB) as the solvent ( with a positively charged protein and few DHB anions) in a box. I have created the .itp and .gro file of DHB using PRODRG. I am able to create the system, but when I try to energy minimiz

Re: [gmx-users] Force field parameters for phosphorylated tyrosine

On 2011-06-13 08:33:15AM -0500, bharat gupta wrote: > thanks for the reply... > > Actually I have found the amber parameters for p-TYR from the following links > : http://www.pharmacy.manchester.ac.uk/bryce/amber#pro > > I am not able to how build the residue topology .. shall I add the topolog

Re: [gmx-users] Force field parameters for phosphorylated tyrosine

bharat gupta wrote: thanks for the reply... Actually I have found the amber parameters for p-TYR from the following links : http://www.pharmacy.manchester.ac.uk/bryce/amber#pro I am not able to how build the residue topology .. shall I add the topology of phosphate only from this to norma

Re: [gmx-users] Force field parameters for phosphorylated tyrosine

thanks for the reply... Actually I have found the amber parameters for p-TYR from the following links : http://www.pharmacy.manchester.ac.uk/bryce/amber#pro I am not able to how build the residue topology .. shall I add the topology of phosphate only from this to normal tyrosine residue ?? !!

Re: [gmx-users] g_confrms and superimposed structures

leila karami wrote: Dear Justin Thanks for your attention My problem was solved. I have a new question. as I said my goal is superposition of averaged md structure and x-ray structure. My simulation is 5 ns. How to obtain the MD structure average for the period 1.5–5 ns? what command?

[gmx-users] g_confrms and superimposed structures

Dear Justin Thanks for your attention My problem was solved. I have a new question. as I said my goal is superposition of averaged md structure and x-ray structure. My simulation is 5 ns. How to obtain the MD structure average for the period 1.5–5 ns? what command? -- Leila Karami Ph.D. stu

Re: [gmx-users] MD - analysis

Kavyashree M wrote: Dear Sir, May be this protein is a disulphide bonded dimer where both the monomers are identical and only 1 disulphide bond is there between them. But other proteins were not like that. May be that is the MAJOR reason for this. but strangely temp, pres, vol, density,

Re: [gmx-users] MD - analysis

Dear Sir, May be this protein is a disulphide bonded dimer where both the monomers are identical and only 1 disulphide bond is there between them. But other proteins were not like that. May be that is the MAJOR reason for this. but strangely temp, pres, vol, density, kinetic, potential and tota

Re: [gmx-users] MD - analysis

Kavyashree M wrote: Dear Sir, What does gmxcheck tell you about the .edr file that is giving weird results? Do the plots look normal? Perhaps a frame got corrupted somewhere along the way. The screen output should print how many frames were considered in the analysis; if i

Re: [gmx-users] g_confrms and superimposed structures

leila karami wrote: Dear Justin very thanks for your reply as you said I have two choices : 1) copy and paste the two models into separate .pdb files. 2) trjconv -sep .no matter which one I choose. the result is the same. because vmd don't open two separate pdb files? Certainly VMD can

Re: [gmx-users] MD - analysis

Dear Sir, > What does gmxcheck tell you about the .edr file that is giving weird > results? Do the plots look normal? Perhaps a frame got corrupted somewhere > along the way. The screen output should print how many frames were > considered in the analysis; if it does not match your expectations

[gmx-users] g_confrms and superimposed structures

Dear Justin very thanks for your reply as you said I have two choices : 1) copy and paste the two models into separate .pdb files. 2) trjconv -sep .no matter which one I choose. the result is the same. because vmd don't open two separate pdb files? is there another way to have 2 structures simu

Re: [gmx-users] MD - analysis

Kavyashree M wrote: Dear Sir, Thanks for your reply. It means "not a number." I've never seen that before from g_energy, but based on the extremely small error estimates, especially for the temperature, I'd suspect you're using extremely tight coupling which may be causing

Re: [gmx-users] g_confrms and superimposed structures

leila karami wrote: Dear gromacs users I know There are two models. VMD loads them as sequential frames such that they can be animated (frame "0" and "1"). I want to have 2 structures simultaneously and not as sequential animation. So copy and paste the two models into separate .pdb files

[gmx-users] g_confrms and superimposed structures

Dear gromacs users I know There are two models. VMD loads them as sequential frames such that they can be animated (frame "0" and "1"). I want to have 2 structures simultaneously and not as sequential animation. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Te

Re: [gmx-users] MD - analysis

Dear Sir, Thanks for your reply. It means "not a number." I've never seen that before from g_energy, but > based on the extremely small error estimates, especially for the > temperature, I'd suspect you're using extremely tight coupling which may be > causing some error. I was thinking such

[gmx-users] g_confrms and superimposed structures

Dear gromacs users I need a figure of superimposed structures. I used g_confrms -f1 1.pdb -f2 2.pdb -o fit.pdb to obtain superimposed structures. when I see fit .pdb using VMD, only 1 structure is seen where as I want to have 2 structures simultaneously. Should I use another commands or flags?

[gmx-users] energy file with g_dipoles

Hi, I have a question regarding g_dipoles. Why does g_dipoles give completely different results of the total dipole moment, when I add or omit the energy file? and which is correct? I mean by providing the energy file or not? and how come I use the energy file when I want to calculate the dipole

Re: [gmx-users] MD - analysis

Kavyashree M wrote: Dear users, While analyzing an MD simulation run for 100ns, for temperature, pressure, volume and density, I got an output like this - Energy Average Err.Est. RMSD Tot-Drift -

Re: [gmx-users] Dissociation of Ligand-reg

ITHAYARAJA wrote: Dear Sir, Greeting! I convey my thanks to your kind reply for rising whatever doubts and troubles in gromacs. I able to do my simulation with desire ligand following your instruction. Now I am interested to simulate the dissociation of bound ligand particularly one mol

[gmx-users] MD - analysis

Dear users, While analyzing an MD simulation run for 100ns, for temperature, pressure, volume and density, I got an output like this - Energy Average Err.Est. RMSD Tot-Drift --- Temperatu

[gmx-users] Regarding H-bond autocorrelation

Hello, I am calculating the H-bond autocorrelation using g_hbond for my system, but after plotting I have observed that the value for c(t) is reaching to negative, as far as I know it can not be negative as the probability can not be negative...please suggest where is the problem.. -- ---

Re: [gmx-users] Force field parameters for phosphorylated tyrosine

On 13/06/2011 7:15 PM, bharat gupta wrote: Hi, Does gromacs and its associated FFs have parameters for phosphorylated tyrosine ?? Probably not. The best place to search is the literature. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] Force field parameters for phosphorylated tyrosine

Hi, Does gromacs and its associated FFs have parameters for phosphorylated tyrosine ?? -- Bharat -- 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 postin

Re: [gmx-users] reg PME usage

On 13/06/2011 6:18 PM, vidhya sankar wrote: Dear mark, I am Typing the Literature Word, as such Although the PME is prefered way to treat Long rang electrostatic interaction it was not used Here Since the overall Charge of Solvated system Had non zero value (-12) Google a

[gmx-users] reg PME usage

Dear mark, I am Typing  the Literature Word, as such Although the PME is prefered way to treat Long rang electrostatic interaction  it was not used Here Since the overall Charge of Solvated system Had non zero value (-12) Also counter ion usually NA+ and CL- added to Neutralize th

[gmx-users] reg electrostatics interaction

Dear sir, Since the overall charge of my system is nonzero can i treat non bonded Reaction using Set of  cutoff distances -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Suppor

Re: [gmx-users] reg PME usage

On 13/06/2011 4:51 PM, vidhya sankar wrote: Dear justin, Thank you for your previous reply. When i study the effect of ionic strength on stability Which Parameter of Electrostatics Should i use? . If I use usual PME Then will it interfere it with result?.