[gmx-users] Problem in protein ligand interaction

Dear Gromacs users, I'm trying to simulate a protein-lipid interaction. Analyzing the simulation, it seems that the lipid does't have enough driving force to reach the binding pocket, since van der Waals forces move the lipind towards the binding pocket whereas electrostatics move the lipid

[gmx-users] Protein stabilization

Dear Gromacs users, I'm trying to perform a protein-lipid complex simulation. While the interaction between these molecules seems reasonable, the protein Root Mean Square Deviation is too high, and I don't know how to stabilice it. Could you recommend me any simulation trick to stabilize the

Re: [gmx-users] Running simulation differences

cs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> en nombre de Justin > Lemkul > Enviado: jueves, 20 de diciembre de 2018 19:52:20 > Para: Discussion list for GROMACS users > Asunto: Re: [gmx-users] Running simulation diff

[gmx-users] RV: Running simulation differences

diciembre de 2018 19:52:20 Para: Discussion list for GROMACS users Asunto: Re: [gmx-users] Running simulation differences On Thu, Dec 20, 2018 at 1:01 PM Gonzalez Fernandez, Cristina < cristina.gonzalezf...@unican.es> wrote: > Hi Justin, > > > Do you think that the differen

Re: [gmx-users] Running simulation differences

de diciembre de 2018 19:52:20 Para: Discussion list for GROMACS users Asunto: Re: [gmx-users] Running simulation differences On Thu, Dec 20, 2018 at 1:01 PM Gonzalez Fernandez, Cristina < cristina.gonzalezf...@unican.es> wrote: > Hi Justin, > > > Do you think that the differen

Re: [gmx-users] Running simulation differences

de Justin Lemkul Enviado: martes, 18 de diciembre de 2018 15:34:07 Para: Discussion list for GROMACS users Asunto: Re: [gmx-users] Running simulation differences On Tue, Dec 18, 2018 at 5:01 AM Gonzalez Fernandez, Cristina < cristina.gonzalezf...@unican.es> wrote: > Hi again Justin, >

Re: [gmx-users] Running simulation differences

the common deviations/errors that are acceptable to a simulation result? Thank you for all your help, C. -Mensaje original- De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se En nombre de Gonzalez Fernandez, Cristina Enviado el: lunes, 17 de diciembre de 2018 18:01 Para: gmx-us

Re: [gmx-users] Running simulation differences

differences On Mon, Dec 17, 2018 at 10:15 AM Gonzalez Fernandez, Cristina < cristina.gonzalezf...@unican.es> wrote: > Hi Kevin, > > Thank you very much for your answer. Do you know how I can set the > "double precision"? > > You would have to recompile and rei

Re: [gmx-users] Running simulation differences

pr *should* converge to the same value. Kevin On Mon, Dec 17, 2018 at 9:53 AM Gonzalez Fernandez, Cristina < cristina.gonzalezf...@unican.es> wrote: > Dear Gromacs users, > > I have tried to run twice the same simulation (same .tpr input file) > in the same workstation, but the re

[gmx-users] Running simulation differences

Dear Gromacs users, I have tried to run twice the same simulation (same .tpr input file) in the same workstation, but the results I obtain significantly differ, for example: (-276.96 ± 40.7 kj/mol) and (-257.25 ± 35.86 kj/mol). Are these differences normal? As these results are different,

Re: [gmx-users] Twin-range and rcoulomb error

On Tue, Nov 27, 2018 at 11:25 AM Gonzalez Fernandez, Cristina < cristina.gonzalezf...@unican.es> wrote: > Dear Gromacs users, > > > I am trying to perform the NVT equilibration of a lipid in water. > According to the manual, for coulombtype=Reaction-Field, rcoulomb must > be

[gmx-users] Twin-range and rcoulomb error

Dear Gromacs users, I am trying to perform the NVT equilibration of a lipid in water. According to the manual, for coulombtype=Reaction-Field, rcoulomb must be higher than rlist. Therefore, I have set rcoulomb=1.4, rvdw=1.4 and rlist=0.8 in order to use twin-range schemes. Besides, I have set

Re: [gmx-users] pcoupl Berendsen

, Gonzalez Fernandez, Cristina wrote: > Hi Justin, > > I have taken a few days in answering you because I was trying to reduce the > discrepancies between the pressure I obtain after simulation and the one I > set in the .mdp file. However, I have no achieve very good results. As

Re: [gmx-users] pcoupl Berendsen

hank you very much for all your help, C. -Mensaje original- De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se En nombre de Justin Lemkul Enviado el: jueves, 8 de noviembre de 2018 14:01 Para: gmx-us...@gromacs.org Asunto: Re: [gmx-users] pcoupl Berendsen On 11/8/18 7:50 AM, Go

[gmx-users] pcoupl Berendsen

Dear Gromacs users, In my simulations, I have specified ref_p= 1bar but after MD simulation I obtain pressures equal to 0.19 bar (even with long simulation times) when using pcoupl=Parrinello-Rahman. I know that Parrinello-Rahman is recommend for production runs and Berendsen for NPT

Re: [gmx-users] pcoupltype

Thank you very much Kevin and Justin for your information -Mensaje original- De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] En nombre de Justin Lemkul Enviado el: miércoles, 31 de octubre de 2018 13:53 Para:

[gmx-users] pcoupltype

Dear Gromacs users, I want to simulate the interaction of a protein and a lipid. I have seen from the tutorials webpage that for the protein-ligand complex (tutorial 5), pcoupltype=isotropic for both the NPT equilibration and the simulation. However, I thought that because of proteins

Re: [gmx-users] Problem in energy calculation

calculation On 10/4/18 11:30 AM, Gonzalez Fernandez, Cristina wrote: > Dear Justin, > > Following your previous email, I have used only index1.ndx in the grompp. But > after running the equilibration, the options of gmx energy don't include > Coul-SR: Other-Water or LJ-SR: Ot

[gmx-users] Complex force field

Dear Gromacs users, I want to estimate the free energy of interaction of a protein-ligand complex by using the Linear Interaction Energy method. For the free lipid simulation, I have used de GROMO96 force field. I know that for the complex I have to used the same force field. With the pdb2gmx

Re: [gmx-users] Problem in energy calculation

On 10/4/18 10:42 AM, Gonzalez Fernandez, Cristina wrote: > Dear Justin, > > Thank you for your suggestions. I have a doubt regarding the groups > generation. I have created the two groups I need as: > gmx make_ndx -f em.gro -o index1.ndx >> 1 >> q > > and > gmx ma

Re: [gmx-users] Problem in energy calculation

l Enviado el: jueves, 4 de octubre de 2018 15:15 Para: gmx-us...@gromacs.org Asunto: Re: [gmx-users] Problem in energy calculation On 10/3/18 7:08 AM, Gonzalez Fernandez, Cristina wrote: > Dear Gromacs users, > > > > > > I want to calculate the van der waals and electrostat

[gmx-users] Problem in energy calculation

Dear Gromacs users, I want to calculate the van der waals and electrostatic interaction energy between a lipid and water. For that purpose, and following the gromacs tutorials I have performed the following steps: * I have include: energygrps = Other Water in the .mdp file to be

[gmx-users] Energy calculations

Dear Gromacs users, I want to determine the electrostatic and van der waals interaction energies of a solute with water. For that purpose, should I create two groups (solute and water) with the gmx make_ndx command or is there another option to calculate these interaction energies? Thank

Re: [gmx-users] Error in NVT equilibration

...@gromacs.org Asunto: Re: [gmx-users] Error in NVT equilibration On 9/19/18 6:14 AM, Gonzalez Fernandez, Cristina wrote: > Hi Justin, > > > I’ve been looking for the non-bonded setting parameters for the GROMOS force > field. I have found that for this force field

Re: [gmx-users] Error in NVT equilibration

AM, Gonzalez Fernandez, Cristina wrote: > Hi, > > > As I am using the GROMOS froce field, I constrained all bonds as suggested. > However, I obtained the same error. > > > I copy the .mdp file in case there are errors and you can help me to find > them: > > >

Re: [gmx-users] Error in NVT equilibration

make the warning go away"), and the warning from grompp may not actually be the source of any problem. -Justin > On Friday, September 14, 2018, 4:07:43 PM GMT+3, Gonzalez Fernandez, > Cristina wrote: > > Dear Gromacs users, > > > I am trying to perform a nvt equilibration, bu

[gmx-users] Error in NVT equilibration

Dear Gromacs users, I am trying to perform a nvt equilibration, but when I generate the .tpr file I get a warning indicating that a bond is oscillating too fast: The bond in molecule-type MOL_1 between atoms 38 C21 and 39 O22 has an estimated oscillational period of 2.4e-02 ps, which is less

Re: [gmx-users] Tolerance and damping coefficient

, Gonzalez Fernandez, Cristina wrote: > Dear Gromacs users, > > > I am trying to reproduce the simulation of a published article and in it the > authors used Particle Meah Ewald for electrostatic interactions with a > relative tolerance of 10^⁻6. I have checked the manual and

[gmx-users] Tolerance and damping coefficient

Dear Gromacs users, I am trying to reproduce the simulation of a published article and in it the authors used Particle Meah Ewald for electrostatic interactions with a relative tolerance of 10^⁻6. I have checked the manual and I only have found tolerance parameters for energy minimization,

[gmx-users] Determine electrostatic and van der waals energies

Dear Gromacs users, I have performed a NPT simulation and I would want to determine the electrostatic and van der Waals energies for the system in order to compare with reference values. I have used g_energy, but the options it offers are: [cid:image002.jpg@01D41EB8.BC55C3A0] I have revised

Re: [gmx-users] Fatal error: Invalid T coupling input: 0 groups, 1 ref-t values and 1 tau-t values

it was not your intent. Mark On Thu, Jul 12, 2018, 17:24 Gonzalez Fernandez, Cristina < cristina.gonzalezf...@unican.es> wrote: > Dear Gromacs users, > > I am trying to perform a NVT equilibration. However, I obtain this error: > > Fatal error: > Invalid T coupling

[gmx-users] Fatal error: Invalid T coupling input: 0 groups, 1 ref-t values and 1 tau-t values

Dear Gromacs users, I am trying to perform a NVT equilibration. However, I obtain this error: Fatal error: Invalid T coupling input: 0 groups, 1 ref-t values and 1 tau-t values I don't understand the problem because I don't have defined any group, I am indicating the ref-t and tau-t for the

[gmx-users] RV: Error energy minimization: No such moleculetype NA

Hi Mark, I have used the changed .top for the grompp. Besides, in the .top file I have writen: ; Include topology for ions #include "gromos43a1.ff/ions.itp" I have checked the "ions.itp" of the gromos43a1.ff folder and NA is included. What else can I do? Best, C. -Mensaje

[gmx-users] Error energy minimization: No such moleculetype NA

Dear Gromacs users, I am trying to perform the energy minimization after adding sodium ions. When I do the grompp to generate the .tpr file that will be used for the energy minimization, I get this error: Fatal error: No such moleculetype NA I have checked the .top file and its true

Re: [gmx-users] No line with moleculetype 'SOL' found the [ molecules ] section

: gmx-us...@gromacs.org Asunto: Re: [gmx-users] No line with moleculetype 'SOL' found the [ molecules ] section On 6/19/18 3:59 AM, Gonzalez Fernandez, Cristina wrote: > Dear Gromacs users, > I am trying adding Na ions: > genion -s ions.tpr -o 1lipidA_solv.g96 -p lipidA_gromacsBien.top &g

[gmx-users] No line with moleculetype 'SOL' found the [ molecules ] section

Dear Gromacs users, I am trying adding Na ions: genion -s ions.tpr -o 1lipidA_solv.g96 -p lipidA_gromacsBien.top -pname NA -np 2 But I get this error: Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file 'lipidA_gromacsBien.top' I have check the .top file and I

Re: [gmx-users] Error in md simulation

match? Mark On Thu, May 31, 2018 at 9:28 AM Gonzalez Fernandez, Cristina < cristina.gonzalezf...@unican.es> wrote: > Dear Gromacs users, > > > I am trying to perform a simulation, and this error apperars: > "131 non-matching atom names. Atom names from .top will be use

[gmx-users] Error in md simulation

Dear Gromacs users, I am trying to perform a simulation, and this error apperars: "131 non-matching atom names. Atom names from .top will be used, atom names from .gro will be ignored" However, I have checked the name of the atoms (atom column) in [atoms] of .top and they are the same as the

[gmx-users] D Gsolv

Dear Gromacs users, Does anyone know the meaning of "D Gsolv" when you plot the area.xvg (output of g_sas)? Any help will highly been appreciated. Best, C. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] g_sas

Dear Gromacs users, I want to calculate the hydrophobic and hydrophilic area of a protein by using the g_sas command. I have used: g_sas -f md.xtc -s md.tpr -o area.xvg -tv volume.xvg However, looking at the area.xvg with xmgrace, I can only see the hydrophobic area not the hydrophilic.

[gmx-users] Simulating protein-lipid interactions

Dear Gromacs users, I want to simulate the interaction of a protein and a lipid. For the protein simulation I have chosen the CHARMM27 force field, because is the one I had selected for the lipid simulation. Does the force field have to be the same for both molecules? How I select the best