[gmx-users] apply protonation state CYS amino acid

Hi Thank you very much for your answer to my former question I want to select CYSH state but we have this option for this amino acid. already I could determine especial state for his,lys,arg,asp by command -his but this command doesn't work for CYS Thanks -- Gromacs Users mailing list * Please se

[gmx-users] apply pH effect on aminoacids

Hi I gave a topology of a protein with pdb2gmx command in next step I change protonation some aminoacids but the topology didn't chage. How could I create new topology? I need to obtain topology protonated aminoacid from other servers? Thanks -- Gromacs Users mailing list * Please search the arch

[gmx-users] binding energy or energy barrier

​Hi all I have done umbrella sampling analysis, a drug was pulled towards the CNT ans encapsulated, then the PMF was calculated, I want to know what is the PMF in this case, is it binding energy or energy barrier against encapsulation? Looking forward to hearing from you Best regards Azadeh --

Re: [gmx-users] reference distance for Lennard Jones interactions

Dear Dr.Lemkul​ Thank you for your answer I get it the cut off radius is distance, when we calculate Lennard Jones (short range) between drug and CNT, what atoms does Gromacs consider for interaction, I mean lennard Jones potential is calculated between two atoms of drug and CNT and then Gromacs

[gmx-users] reference distance for Lennard Jones interactions

​Hi I have calculated Lennard Jones interaction between drug and Carbon Nano tube by defining "energygroups" and I got the potential by "gmx energy" I have a question, in this figure I have potential versus distance (r), what is the distance? in Lennard Jones equation the distance defines between

[gmx-users] interpretation of force in pulling simulation

​Hi all I 've translocated drug molecule into the different carbon nanotubes in a pulling simulation and the force was obtained , can I tell that the case that has maximum difference force at CNT end, has minimum energy barrier? In real I can't find relationship between this force and energy barr

[gmx-users] radial distribution function

​​​Hi all I want to investigate adsorption drug on CNT,, the radius of CNT is 1 nm, RDF and distance of each drug around CNT were calculated, but I couldn't attach these picture in this email, I saw, all drugs adsorbed on CNT surface at distance 1.5 nm, but I couldn't understand why the intense

[gmx-users] radial distribution function

​Hi all when we calculate RDF, we have g(r) versus radius, please tell me, what is this radius, is it the distance between center of mass of two component or is it the radius of a sphere that is consider for probability of finding molecules, what is difference between -com and -xy? if I want to c

[gmx-users] Lennrd-Jones potential in Gromos force field

​I get it, your guidance helped me, Thank you very much -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit ht

[gmx-users] Lennrd-Jones potential in Gromos force field

​Thank you Dr.Abraham for your answer I used different functional groups for functionalization CNT, I determined polarity with dipole moment that can be calculated using partial charges by VMD, my goal from these question is to find a way to separate type of interaction between drug and functi

[gmx-users] Lennrd-Jones potential in Gromos force field

​Hi I have another question, I used gmx energy to evaluate LJ and electrostatic interaction, as before discussion LJ is meaningless physically, is there another module that can predict , polar and non polar interactions accurately? is this meaningless that you mentioned according to Gromos forc

[gmx-users] Lennrd-Jones potential in Gromos force field

​I get it now, Thank you very much for your help. -- This email was Anti Virus checked by Security Gateway. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Suppor

[gmx-users] Lennrd-Jones potential in Gromos force field

​Hi Dr.Lemkul Thank you very much for your answer, it means that, LJ contains attraction and repulsion parts that calculate correspond distance, distance and epsilon, in my paper, what can I called what obtained from LJ-SR, is it vdW ? Thanks in advance for your time and your help Regards Azadeh

[gmx-users] Lennrd-Jones potential in Gromos force field

​Hi Dr.Abraham Thank you very much for your answer, I couldn't recognize my problem that , what does LJ-SR indicate in gmx energy module, vdw, polar-polar, nonpolar-nonpolar or other interactions? Thanks in advance for your answer and your help Regards Azadeh -- This email was Anti Virus check

[gmx-users] Lennrd-Jones potential in Gromos force field

​Hi all I've simulated interaction of functionalized carbon nanotubes with drug with Gromos 54a7 force field, by gmx energy module and defining enegy grps I obtained LJ-SR , short range Lennad-jones potential between drug and CNT, in my system there are different interavtions, polar-polar, nonpo

[gmx-users] deformation in carbon nanotube structure

Hi every one I want to investigate carbon nanotube, because my CNT is large I couldn't get topology from automatic servers, then I used gmx X2top to make topology and I corrected bond and angle constant with data from paper, in first part of my simulation I don't apply any restraint on CNT beca

[gmx-users] deformation in structure of carbon nanotube

Hi every one I want to investigate carbon nanotube, because my CNT is large I couldn't get topology from automatic servers, then I used gmx X2top to make topology and I corrected bond and angle constant with data from paper, in first part of my simulation I don't apply any restraint on CNT beca

Re: [gmx-users] problem with inflategro

Hi Dr.Lemkul Thank you very much for your answer, I think input file is correct, when I performed infaltegro again, I found this error Argument "C1" isn't numeric in printf at inflategro.pl line 502. Argument "C2" isn't numeric in printf at inflategro.pl line 502. Argument "C3" isn't numeric in

[gmx-users] problem with inflategro

Hi all when I used inflategro in KALP in DPPC tutorial, I had no problem, but in my system I have a receptor in bilayer , I have 1152 DPPC when I use inflategro in systeminflated.gro file some of lines is duplicated, this happens for 200 DPPC, as follow: 35DPPC 0 1716.798 16.173 4

[gmx-users] problem with inflategro

Hi all when I used inflategro in KALP in DPPC tutorial, I had no problem, but in my system I have a receptor in bilayer , I have 1152 DPPC when I use inflategro in systeminflated.gro file some of lines is duplicated, this happens for 200 DPPC, as follow: 35DPPC 0 1716.798 16.173 4

[gmx-users] definition electrical field in a special position

Hi all when I use E_z, it applies an electric field in the z direction, but I want to apply that in special thickness in the z direction, not in all length, is there any way to do it? Thanks in advance Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- Gromacs Use

Re: [gmx-users] using enegygrps

Hi Dr.Lemkul Thank you very much for your answer, it was very great help for me Thank you Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List befor

Re: [gmx-users] using enegygrps

Hi Dr.Lemkul you said, the breaking molecule occured because of period boudary condition, isn't it a problem? because before your answer I thought I must select bigger box in order to the breaking won't occur. but now I understand the beaking isn't a problem. I have another question, what is d

Re: [gmx-users] using enegygrps

Hi Dr.Lemkul Thank you very much for your answer and your time I 'm using Gromos 54a7 force field, How can I find my force field is parametrized in such a way that the nonbonded energy decomposition has some physical meaning? Thank you Regards Azadeh -- This email was Anti Virus checked b

[gmx-users] using enegygrps

Hi all I want to investigate interaction drug and bilayer for more detailed investigation I want to use energygrps for functional group of drug to find out which part of drug has more interaction. is energygrps good tool? Thank you very much Regards Azadeh -- This email was Anti Virus chec

Re: [gmx-users] pressure coupling error in umbrella sampling

Hi Dr.Lemkul Thank you very much for your answer I get it now, before your answer I run system with -maxwarn 1, I saw trajectory in vmd , my drug molecule break in middle of run and then corrected, is it wrong? has it occured because using maxwran? is vmd an appropriate tool for detect trajec

Re: [gmx-users] pressure coupling error in umbrella sampling

Hi Dr.Abraham Thank you very much for your answer yas I 've extacted configuration with 0.2 nm distance and when I want to run NPT for first configuration,I gave that error. I didn't undersatnd this mdp file for this step, I got this file from umbrella sampling tutorial and I adjusted for my s

[gmx-users] pressure coupling error in umbrella sampling

Hi all I 'm doing umbrella sampling, I 've selected initial configuration , in NPT step I have this error WARNING 1 [file npt_umbrella.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unsta

Re: [gmx-users] dimension of fulling force in pulling simulation

Dear Alex Thank you very much for your answer I know kj per nm is force but I can convert when it is per mol. kj /(nm mol) do I calculate mol of molecules in system? soory if my question is simple Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- Gromacs Users

[gmx-users] dimension of fulling force in pulling simulation

Hi I 've done a pulling simmulation and I 've get pullf.xvg file, dimension of force is kJ/mol/nm I didn't understand, shouldn't it be in N(newton) dimension? why per mol?please guide me Thank you very much Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- Gromac

Re: [gmx-users] gmx enenrgy

Hello Dr.Lemkul Thank you very much for your answer I try to do it. Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't p

[gmx-users] gmx enenrgy

Hi all when we use "gmx energy" what is the difference between LJ-(SR), LJ-14, Coulomb-14, Coulomb(SR)? those mentioned energies, give us energy interaction of total system. right? if I want to determine interaction enenrgy for example, LJ, between two special species, not in total system, wha

Re: [gmx-users] difference between force constants in various force field

Hello Dr.Lemkul I get it. Thank you very much for your answer. Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? R

[gmx-users] difference between force constants in various force field

Hi every one I have a question I want to obtain topology of carbon nano tube with x2top but I must determine the value of bond strength and angle constant. I think we have a bond carbon-carbon that stretches with a constant force for example in amber force field this constant is 392459 kj /(m

Re: [gmx-users] lambda value for free energy calculation

Hi Dr.Abraham Thank you very much for your answer excuse me but, I didn't understand I want to calculate free energy of drug in water and I want to consider VDW,coulombic and bonding interation with these lambda value vdw_lambdas = 0.00 0.05 0.10 ... 1.00 1.00 1.00 ... 1.00 1.00 1.00 1.00 .

[gmx-users] lambda value for free energy calculation

Hi all I have aquestion about free energy calculation as in tutorial be said if we want to consider coloumbic interaction we must define lambda as follows: vdw_lambdas = 0.00 0.05 0.10 ... 1.00 1.00 1.00 ... 1.00 coul_lambdas = 0.00 0.00 0.00 ... 0.00 0.05 0.10 ... 1.00 if I want to consider

[gmx-users] KALP in DPPC

Hi Dr.Lemkul Thank you very much for your answer I will select 310 kelvin becauase I want to investigate physiological condition. in tutorial we've used semiisotropic pressure coupling and normal and lateral pressure are determined 1 bar. why? is it related to surface tension? if we want to

[gmx-users] KALP in DPPC

Hi all in tutorial KALP in DPPC, why we set temperature above the phase transittion temperature whereas physiological temperature is 310 kelvin. I want too investigate interaction of carbon nano tube and DPPC bilayer and I think , I should set temperature to 310. is that right? Thank you v

[gmx-users] calculation of surface tension

Hi all I want to calculate surface tension in lipid bilayer. I read manual and mailing list message and I have some question: for calclation surface tension we should use Berendsen barostate with semiisotropic coupling , in mdp file: ; Pressure coupling is on pcoupl = Berendsen ; Pre

Re: [gmx-users] pressure coupling

Hello Dr.Abraham Thank you very much for your answer Your answer was very clear and I understood it. it was very helpful. Best regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Suppo

Re: [gmx-users] pressure coupling

Hello Dr.Lemkul Thank you very much for your help and your answer my average pessure is 1.5 bar and it fluctuates + and - 295 bar . as your guide, I will consider it near to 1 bar. I didn't know what I should do I thought pressure must converge to 1 bar exactly and 1.5 isn't appropriate I ge

[gmx-users] determine surface tension

Hi all I want to calculate surface tension in lipid bilayer. I read manual and mailing list message and I have some question: for calclation surface tension we should use Berendsen barostate with semiisotropic coupling , in mdp file: ; Pressure coupling is on pcoupl = Berendsen ; P

[gmx-users] determine surface tension

Hi all I want to calculate surface tension in lipid bilayer. I read manual and mailing list message and I have some question: for calclation surface tension we should use Berendsen barostate with semiisotropic coupling , in mdp file: ; Pressure coupling is on pcoupl = Berendsen ;

[gmx-users] pressure coupling

Hi all I want to investigate carbin nanotube as drug carrier I want to fnctionalize CNT and compare results with experimental but I have a problem functionalization performed in constant pressure 1 atm . Pressure in my system converges hard and I try several times I changed time step , number o

[gmx-users] determine surface tension on carbon nanotube

Hello I want to determine surface tension of carbon nanotube, I read in manual that the interface must be parallell to x-y plane but in CNT we have a cylindrical interface. I have two system 1-CNT in water 2- CNT and polyethylene glycol(PEG) , How can I determine that I want surface tension

[gmx-users] recognition two phase in gromacs

Hello every body I have a question, How does gromacs recognize different phases? There are carbon nanotube , polymer and solvent in my system, if temprature would be lower than Tg of polymer, does gromacs define polymer as a solid? Any suggestion will be appreciated. Thank you very much. Regar

[gmx-users] determine surface tension on carbon nanotube

Hello I want to determine surface tension of carbon nanotube, I read in manual that the interface must be parallell to x-y plane but in CNT we have a cylindrical interface. I have two system 1-CNT in water 2- CNT and polyethylene glycol(PEG) , How can I determine that I want surface tension in

[gmx-users] recognition two phase in gromacs

Hello every body I have a question, How does gromacs recognize different phases? There are carbon nanotube , polymer and solvent in my system, if temprature would be lower than Tg of polymer, does gromacs define polymer as a solid? Any suggestion will be appreciated. Thank you very much. Rega