Re: [gmx-users] some problems when using g_membed

On 18/10/2011 2:08 PM, mirc...@sjtu.edu.cn wrote: > Dear All: > > I am using g_membed command to insert a protein into a membrane > bilayer, however, when I run the following command: > > g_membed -f input.tpr -p topology.top -xyinit 0.1 -xyend 1.0 -nxy 1000 > > I encountered the following errors:

[gmx-users] do Shell Molecular Dynamics with GROMACS

how can i do if i want to do Shell Molecular Dynamics(Drude ) with GROMACS VERSION 4.0.7? I only find you should set "emtol: (1.0) niter: (20) fcstep: (0) [ps2]" in *.mdp file .(GROMACS_4.0 manual) But how i can write the *.gro and *.top ? Are they smae with the traditional MD? And i can not fi

[gmx-users] some problems when using g_membed

Dear All: I am using g_membed command to insert a protein into a membrane bilayer, however, when I run the following command: g_membed -f input.tpr -p topology.top -xyinit 0.1 -xyend 1.0 -nxy 1000 I encountered the following errors: Program g_membed, VERSION 4.5.4 Source code file: constr.c

Re: [gmx-users] box dimension

On 18/10/2011 11:48 AM, Nilesh Dhumal wrote: I used -pbc nojump to remove pbc effect. Please read trjconv -h about -pbc nojump. If molecules can't jump, then they must diffuse. You can't have both. Mark trjconv 3.trr -s 3.tpr -pbc nojump -o 500-11.pdb Basically I want to find the conf

Re: [gmx-users] box dimension

I used -pbc nojump to remove pbc effect. trjconv 3.trr -s 3.tpr -pbc nojump -o 500-11.pdb Basically I want to find the conformer close to center of box. Nilesh On Mon, October 17, 2011 6:36 pm, Mark Abraham wrote: > On 18/10/2011 7:05 AM, Nilesh Dhumal wrote: > >> Hello, >> >> >> I have saved

Re: [gmx-users] acylation of peptide

On 18/10/2011 2:57 AM, ??? wrote: No I need your help in any way, antechamber is not only the way I could do it, I think...I just showed you that I tried something before I wrote you a letter. It is not necessary to use amber forcefield, but I don't think that prodrg is a good cho

Re: [gmx-users] Updating charges on-the-fly

On 18/10/2011 5:40 AM, J. Nathan Scott wrote: Hello fellow GMX users, I've been digging in the archives and haven't yet found a good response to this question, so I thought I'd ask again, since I see from a post just last month others are still interested in this subject as well. Is it possib

Re: [gmx-users] box dimension

On 18/10/2011 7:05 AM, Nilesh Dhumal wrote: Hello, I have saved the coordinates of snapshot from trajectory in pdb file. The dimesnion of box in pdb file are 32.805 32.805 32.805 90.00 90.00 90.00 P 1 I am trying to find atoms close to center of box. there are atoms whose distance fr

Re: [gmx-users] REMD and GBSA

On 18/10/2011 4:58 AM, Ben Reynwar wrote: On Fri, Oct 14, 2011 at 9:11 AM, Mark Abraham wrote: On 14/10/2011 10:12 AM, Ben Reynwar wrote: Hi gromacs list, I'm about to start some REMD simulations using generalized Born solvent on a protein of about 5000 atoms. I have two questions, the first

Re: [gmx-users] solvents in gmx

Yao Yao wrote: Hi Gmxers, Is there a way I can check all the kinds of solvents in gromacs? Apart from water, ethanol, ..., are there any Glycerol, Treholose, There likely aren't many. Anything available would be in the force field subdirectory for whatever force field you want. Ot

[gmx-users] solvents in gmx

Hi Gmxers, Is there a way I can check all the kinds of solvents in gromacs? Apart from water, ethanol, ..., are there any Glycerol, Treholose, Thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at h

Re: [gmx-users] trjconv:solute at the center

Hi Nilesh, To center the solute with respect to the solvent, first center the solute in the box, and then put the solvent in the box. Mind that that involves two passes of trjconv. If 'no pbc effect' means no wrapping over the boundaries, yes you can use -dump with -pbc nojump to save a snapshot.

Re: [gmx-users] Simulation of membrane protein

James Starlight wrote: Justin I can't access the file, so I don't know. 20 iterations still doesn't sound like enough for the tutorial system, unless you shrunk faster than what was recommended. 20 iteration was a simple example. It means that many iterations produced more ac

[gmx-users] box dimension

Hello, I have saved the coordinates of snapshot from trajectory in pdb file. The dimesnion of box in pdb file are 32.805 32.805 32.805 90.00 90.00 90.00 P 1 I am trying to find atoms close to center of box. there are atoms whose distance from center is more that ~17 A. My center coordi

Re: [gmx-users] Simulation of membrane protein

Justin > >> > I can't access the file, so I don't know. 20 iterations still doesn't > sound like enough for the tutorial system, unless you shrunk faster than > what was recommended. 20 iteration was a simple example. It means that many iterations produced more accuracy results in comparison to

Re: [gmx-users] trjconv:solute at the center

Ya, I want to center solute w.r.t to the solvent. I have more question, if I want to save the coordinates of a snapshot with no pbc effect, can I use -pbc nojump in trjconv. nilesh On Mon, October 17, 2011 1:34 pm, Tsjerk Wassenaar wrote: > Hey :) > > > The reference plays no role in centering.

[gmx-users] Updating charges on-the-fly

Hello fellow GMX users, I've been digging in the archives and haven't yet found a good response to this question, so I thought I'd ask again, since I see from a post just last month others are still interested in this subject as well. Is it possible in Gromacs to periodically update/change the cha

Re: [gmx-users] lipid membrane slicing

Poojari, Chetan wrote: Hi Justin, Using make_ndx on the trajectory file (output from trjorder), and listing out different lipids i did see the lipids arranged based on the distance from protein. Now i want to choose lipids within 0.5nm from protein for my analysis. As in the index file th

RE: [gmx-users] lipid membrane slicing

Hi Justin, Using make_ndx on the trajectory file (output from trjorder), and listing out different lipids i did see the lipids arranged based on the distance from protein. Now i want to choose lipids within 0.5nm from protein for my analysis. As in the index file the lipids are listed based o

Re: [gmx-users] REMD and GBSA

On Fri, Oct 14, 2011 at 9:11 AM, Mark Abraham wrote: > On 14/10/2011 10:12 AM, Ben Reynwar wrote: >> >> Hi gromacs list, >> >> I'm about to start some REMD simulations using generalized Born >> solvent on a protein of about 5000 atoms.  I have two questions, the >> first of which is about gromacs,

Re: [gmx-users] trjconv:solute at the center

Hey :) The reference plays no role in centering. But I guess that Nilesh expects centering of the solute w.r.t. to the solvent, or is looking at the wrong center (tric/rect). Cheers, Tsjerk On Oct 17, 2011 7:06 PM, "Justin A. Lemkul" wrote: Nilesh Dhumal wrote: > > Thanks Justin, > > Still so

Re: [gmx-users] trjconv:solute at the center

Nilesh Dhumal wrote: Thanks Justin, Still solute is not at center. Is your reference frame (i.e. the .tpr file) centered? If not, centering likely won't work as desired. I assumed that it was centered, per normal system building procedures. -Justin Nilesh On Mon, October 17, 2011

Re: [gmx-users] Simulation of membrane protein

James Starlight wrote: Dear Justin, After 20 iterations I've obtained structure like this http://www.sendspace.com/file/gyyj38 I suppose that this variat is more closely to correct form :) I can't access the file, so I don't know. 20 iterations still doesn't sound like enough for the

Re: [gmx-users] Interaction energy

Steven Neumann wrote: Dear Gmx Users, I would like to calculate the interaction energy (LJ and electrostatic) between each residue and my ligands (10 ligands in the system). I would like to see what is the contribution of electrostatic and vdW interactions between ligand and each of my res

Re: [gmx-users] topologies for POPE and DMPE

Hi Pramod, Please keep all general queries and questions on the GROMACS mailing list. For CHARMM27, POPC can be found as an rtp entry. This means a topology can be generated using pdb2gmx. It is easiest if you do this using one POPC lipid and then make an itp from the top. A CHARMM POPC bilaye

Re: [gmx-users] Simulation of membrane protein

Dear Justin, After 20 iterations I've obtained structure like this http://www.sendspace.com/file/gyyj38 I suppose that this variat is more closely to correct form :) But during solvation via GenBox I've obtained that error One of the box vectors has become shorter than twice the cut-off length

[gmx-users] Re: gmx-users Digest, Vol 90, Issue 82

No I need your help in any way, antechamber is not only the way I could do it, I think...I just showed you that I tried something before I wrote you a letter. It is not necessary to use amber forcefield, but I don't think that prodrg is a good choice for this task, though the only modification of

Re: [gmx-users] trjconv:solute at the center

Thanks Justin, Still solute is not at center. Nilesh On Mon, October 17, 2011 11:27 am, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> In 2nd step I choose system instaed of solvent. >> >> >> I could not make the solute at the center. >> >> > > Don't use -b and -e when running trjconv

[gmx-users] Interaction energy

Dear Gmx Users, I would like to calculate the interaction energy (LJ and electrostatic) between each residue and my ligands (10 ligands in the system). I would like to see what is the contribution of electrostatic and vdW interactions between ligand and each of my residue. I thought to use g_energ

Re: [gmx-users] High temperature Simulation

Kavyashree M wrote: Ok, The protein I am going to simulate is from a hyperthermophilic organism which lives in deep oceanic thermal vents. so in the deep vents the pressure will be enormous. even though I do not have much information about the magnitude of pressure in that site and inside the c

Re: [gmx-users] trjconv:solute at the center

Nilesh Dhumal wrote: In 2nd step I choose system instaed of solvent. I could not make the solute at the center. Don't use -b and -e when running trjconv. I have found that PBC routines are not always correctly applied when parsing out sections of the trajectory. This can affect your ab

Re: [gmx-users] High temperature Simulation

Ok, The protein I am going to simulate is from a hyperthermophilic organism which lives in deep oceanic thermal vents. so in the deep vents the pressure will be enormous. even though I do not have much information about the magnitude of pressure in that site and inside the cell of that organism.. I

Re: [gmx-users] trjconv:solute at the center

In 2nd step I choose system instaed of solvent. I could not make the solute at the center. Thanks NIlesh On Mon, October 17, 2011 11:05 am, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Justin, >> >> >> I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328 >> atoms).

Re: [gmx-users] High temperature Simulation

Kavyashree M wrote: Hello, I am sorry those were two different questions.. I wanted to know what this statement actually mean? "The set pressure should reflect whatever system you are trying to model." You haven't fully explained what exactly you're trying to do yet, so I'm taking a stab

Re: [gmx-users] High temperature Simulation

Hello, I am sorry those were two different questions.. I wanted to know what this statement actually mean? "The set pressure should reflect whatever system you are trying to model." Thank you With Regards Kavya > > I don't see the connection to my comment about pressure, but I'll address > this

Re: [gmx-users] High temperature Simulation

Hello, Yes, I have come across that but If the temperature is below the boiling point its fine. But if it crosses the boiling temperature in order keep the water as liquid isnt it necessary to increase the pressure. I understand that the water models do not exactly predict the transition temperatu

Re: [gmx-users] trjconv:solute at the center

Nilesh Dhumal wrote: Justin, I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328 atoms). 1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx -o 4-600.xtc here I choose group 0:system (3328 atoms) 2. trjconv -f 4-600.xtc -s 3.tpr -n 500-1.ndx -center

Re: [gmx-users] High temperature Simulation

Kavyashree M wrote: Hello, The set pressure should reflect whatever system you are trying to model. This statement is not very clear to me.. But when the mdout.mdp file after grompp during energy minimization is examined it says - gen-vel = no gen-temp

Re: [gmx-users] trjconv:solute at the center

Justin, I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328 atoms). 1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx -o 4-600.xtc here I choose group 0:system (3328 atoms) 2. trjconv -f 4-600.xtc -s 3.tpr -n 500-1.ndx -center -o 4-600-1.xtc For Cent

Re: [gmx-users] High temperature Simulation

Hello, The set pressure should reflect whatever system you are trying to model. > This statement is not very clear to me.. But when the mdout.mdp file after grompp during energy minimization is examined it says - gen-vel = no gen-temp = 300 gen-seed

Re: [gmx-users] Spherical constraint (spherical force)

Hi Mikhail, we hard-coded the flat-bottom potential into bondfree.c which is in src/gmxlib. I send you the source file in a separate e-mail. The patch will replace all position restraints by a flatt-bottom spherical potential with a flat radius of 1.4nm. If you want a different radius you'll

Re: [gmx-users] Simulation of membrane protein

James Starlight wrote: Ok, James thank you It seems that I should to wite some script for too many iterations e.g perl inflategro.pl minimized1.gro 0.95 DPPC 0 shrinked1.gro 5 area_shrink1.dat grompp -f minim.mdp -c shrinked1.gro -p topol.top -o minimized2.tpr mdrun

Re: [gmx-users] Spherical constraint (spherical force)

On 17/10/2011 11:41 PM, Mikhail Stukan wrote: Dear gmx-user, I would like to simulate an isolated drop of water (without PBC). To prevent water molecules form evaporation I would like to create a spherical constraint around the system. In recent article in PNAS (Caleman, Hub, van Maaren, v

Re: [gmx-users] Simulation of membrane protein

Ok, James thank you It seems that I should to wite some script for too many iterations e.g perl inflategro.pl minimized1.gro 0.95 DPPC 0 shrinked1.gro 5 area_shrink1.dat grompp -f minim.mdp -c shrinked1.gro -p topol.top -o minimized2.tpr mdrun -v -deffnm minimized2 perl inflategro.pl minimized

[gmx-users] Spherical constraint (spherical force)

Dear gmx-user, I would like to simulate an isolated drop of water (without PBC). To prevent water molecules form evaporation I would like to create a spherical constraint around the system. In recent article in PNAS (Caleman, Hub, van Maaren, van der Spoel, v. 108, 6838 (2011)) where the aut

Re: [gmx-users] Link to Intel MKL (fftw) via cmake options

> --- [CMakeCache.txt] - > > ... > > //Flags used by the compiler during all build types > CMAKE_CXX_FLAGS:STRING=' -msse2 -ip -funroll-all-loops -std=gnu99  ' > > //Flags used by the compiler during release builds. > CMAKE_CXX_FLAGS_RELEASE:STRING=-mtune

[gmx-users] RE:Free energy methods Protein-Protein

Dear All, I tried to post this once before. In any case; Basically I am doing free energies quickly, and then plan on doing pull runs. This former is simply EQ all the way to NPT (700-1000 PS +), then a 5 PS run for the bound, then unbound system. Energy differences are taken as the differ

Re: [gmx-users] cyclosporine A

On 17/10/2011 5:01 PM, Алексей Раевский wrote: Hi! I need an advice concerninng topology building of such substance like cyclosporine A. I've tried to make it with antechamber tool, cause I wanted to use amber99sb forcefield. But the program gave me an error in the begining and no results in t

Re: [gmx-users] High temperature Simulation

On 17/10/2011 10:58 PM, bipin singh wrote: I have not understood what you mean by "Energy minimization is (theoretically) at 0 K, as there are no velocities and it is not a true dynamical process." It is clear to me that at 0K there would be no velocities but then why during minimization we expec

Re: [gmx-users] High temperature Simulation

In the energy minimisation step, any "conformational rearrangement" taking place is not a function of time, it is just an algorithm for reaching a basin of minimum energy: (http://www.gromacs.org/Documentation/Terminology/Energy_Minimisation), hence there are not velocities in the atoms of the sy

Re: [gmx-users] Simulation of membrane protein

James Starlight wrote: James, As the consequence the correct orientation of the peptide in the membrane as well as futher solvation are caused many questions :) Firsly, following by tutorial guide I've done orientation of KALP peptide in the membrane by 1- perl inflategro.pl

Re: [gmx-users] High temperature Simulation

I have not understood what you mean by "Energy minimization is (theoretically) at 0 K, as there are no velocities and it is not a true dynamical process." It is clear to me that at 0K there would be no velocities but then why during minimization we expect some conformational rearrangement of side c

Re: [gmx-users] Simulation of membrane protein

James, As the consequence the correct orientation of the peptide in the membrane as well as futher solvation are caused many questions :) Firsly, following by tutorial guide I've done orientation of KALP peptide in the membrane by 1- perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro

Re: [gmx-users] High temperature Simulation

Well,as I found in literatures people have used same( 1 atm) pressure at high temperature simulations(NPT simulations). with different water models.As most of the force field parameters are determined generally at 300K and 1 atm. What would be the the possible drawbacks of using the same pressure(o

Re: [gmx-users] High temperature Simulation

Kavyashree M wrote: Thank you, What about the pressure that need to be used at that temperature (for a system of a protein in tip4p water) The set pressure should reflect whatever system you are trying to model. -Justin Thank you With Regards Kavya On Mon, Oct 17, 2011 at 3:29 PM, bipin

Re: [gmx-users] High temperature Simulation

bipin singh wrote: As far as I know we do energy minimization at room temperature only. Energy minimization is (theoretically) at 0 K, as there are no velocities and it is not a true dynamical process. Only during equilibration (NVT and NPT) we use high temperature for maintaining proper

Re: [gmx-users] Simulation of membrane protein

James Starlight wrote: Justin Sure, you could do all of it within a shell script that loops the commands and checks the printed output. As I understood in that iterations only step with scalling by factor 0.95 and futher energy minimization must be included until desired S per lip

Re: [gmx-users] trjconv:solute at the center

Nilesh Dhumal wrote: Hello, I have system with solute is surrounded by 256 solvent molecules. I run the simulation for 20 ns. I save the snap shot at 500 ps using following command. trjconv -f 3.trr -s 3.tpr -n 500-1.ndx -b 500.0 -e 501.0 -dt 1.0 -pbc nojump -center -o 500-11.pdb I tried t

Re: [gmx-users] High temperature Simulation

Thank you, What about the pressure that need to be used at that temperature (for a system of a protein in tip4p water) Thank you With Regards Kavya On Mon, Oct 17, 2011 at 3:29 PM, bipin singh wrote: > As far as I know we do energy minimization at room temperature only. > Only during equilibra

Re: [gmx-users] topologies for POPE and DMPE

Hi Roy, PE lipids are less frequently used than PC ones and there are fewer topologies available. Also it has been shown that using the Berger PC lipid topologies (the most frequently used united-atom PC lipids) and simply changing the CH3 atoms in the head group to H is not a good approach f

Re: [gmx-users] High temperature Simulation

As far as I know we do energy minimization at room temperature only. Only during equilibration (NVT and NPT) we use high temperature for maintaining proper density before starting the final production run. On Mon, Oct 17, 2011 at 15:15, Kavyashree M wrote: > Dear users, > > For simulating a prote

[gmx-users] High temperature Simulation

Dear users, For simulating a protein at high temperature (more than 300K, less than 400K) using OPLSAA forcefield, what are the parameters other than Temperature that need to be taken care of? Does the energy minimization step also needs to be done at high temperature? (here my aim is not to simul

Re: [gmx-users] CHARMM GUI to Gromacs

There is already tutorial for creating lipid bilayer and insertion of protein into that for GROMACS http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html Why you have used Charmmgui I am not able to understand. You can get some useful topologies from bel

[gmx-users] CHARMM GUI to Gromacs

Dear all, I would like to simulate my protein in a lipid bilayer using gromacs 4.5.4, and a forcefield of gromos96. However i don't have the topologies files for lipid bilayer for POPE and DMPE. Anybody knows where can i get the topologies file for POPE and DMPE ? Before that, i had actually use

Re: [gmx-users] Implicit solvation

Check the below link: http://www.gromacs.org/Documentation/Terminology/Implicit_Solvent On Mon, Oct 17, 2011 at 13:47, Soumya Lipsa Rath wrote: > I am a new gromacs user. I wanted to simulate a membrane protein without the > lipid bilayer using the IMM1 force field of CHARMM27. I really would > a

[gmx-users] Implicit solvation

I am a new gromacs user. I wanted to simulate a membrane protein without the lipid bilayer using the IMM1 force field of CHARMM27. I really would appreciate if someone can help me solve this or direct me towards implicit solvation tutorial in gromacs Regards, Soumya ** -- gmx-users mailing list

Re: [gmx-users] Simulation of membrane protein

Justin Sure, you could do all of it within a shell script that loops the commands > and checks the printed output. As I understood in that iterations only step with scalling by factor 0.95 and futher energy minimization must be included until desired S per lipid will be reached. Could you provi