Re: [gmx-users] Query regarding membrane-peptide simulation

On 8/19/13 6:27 AM, Aditya Padhi wrote: Dear Gromacs Users, I am new to Gromacs. Recently, I started working with Gromacs. I want to study the mechanism of interaction of certain peptides that are known to interact with membranes such as DOPC, POPC and so on. I have two sets of peptide

[gmx-users] Query regarding membrane-peptide simulation

Dear Gromacs Users, I am new to Gromacs. Recently, I started working with Gromacs. I want to study the mechanism of interaction of certain peptides that are known to interact with membranes such as DOPC, POPC and so on. I have two sets of peptides; out of which, one set of peptides are know

Re: [gmx-users] query on replica exchange

Hi, You can only have as many replicas as you have MPI processes available, but you can find out how to configure your MPI to allow such over-subscription of your hardware. Mark On May 31, 2013 6:28 AM, "Sanku M" wrote: > Hi, > I am wondering if there is a way I can use twice more number of r

[gmx-users] query on replica exchange

Hi,   I am wondering if there is a way I can use twice more number of replica than the number of CPU is available so that each replica will run at 50 % CPU usage..For example if I have 48 replica and have 24 CPUs, is it a possibility to perform Replica exchange in gromacs ? I was using gromacs4.

Re: [gmx-users] query respect to perl distances.pl

On 5/11/13 12:38 AM, Arunima Shilpi wrote: Respected Sir Presently my work includes umbrella sampling for protein ligand interaction. The components of md_pull.mdp is title = Umbrella pulling simulation define = -DPOSRES_B ; Run parameters integrator = md dt = 0.002 tinit

[gmx-users] query respect to perl distances.pl

Respected Sir Presently my work includes umbrella sampling for protein ligand interaction. The components of md_pull.mdp is title = Umbrella pulling simulation define = -DPOSRES_B ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 500 ps nst

Re: [gmx-users] query for gromacs-4.5.4

One cannot run an arbitrary simulation on an arbitrary number of processors. The particles in the simulation have to get mapped to processors that handle them. This is done in small parcels called domains. The atoms move between domains, and so the responsibility moves too. If the velocities are hi

Re: [gmx-users] query for gromacs-4.5.4

Hello Sir, The job runs for 8 processes given 1 , 2 or 8 nodes but not for more than that. 16 proceses : Segmentation fault and For 32 processes it gives : "Fatal error : 467 particles communicated to PME node 4 are more than 2/3 times the cut off out of the domain decomposition cell of their char

Re: [gmx-users] query for gromacs-4.5.4

It could be anything. But until we see some GROMACS diagnostic messages, nobody can tell. Mark On Tue, Mar 12, 2013 at 10:08 AM, Chaitali Chandratre wrote: > Sir, > > Thanks for your reply > But the same script runs on some other cluster with apprx same > configuration but not on cluster on

Re: [gmx-users] query for gromacs-4.5.4

Sir, Thanks for your reply But the same script runs on some other cluster with apprx same configuration but not on cluster on which I am doing set up. Also job hangs after some 16000 steps but not come out immediately. It might be problem with configuration or what? Thanks... Chaitali On T

Re: [gmx-users] query for gromacs-4.5.4

They're just MPI error messages and don't provide any useful GROMACS diagnostics. Look in the end of the .log file, stderr and stdout for clues. One possibility is that your user's system is too small to scale effectively. Below about 1000 atoms/core you're wasting your time unless you've balanced

Re: [gmx-users] query for gromacs-4.5.4

Hello Sir, Actually I have been given work to setup gromacs-4.5.4 in our cluster which is being used by users.I am not gromacs user and not aware of its internal details. I have got only .tpr file from user and I need to test my installation using that .tpr file. It works fine for 2 nodes 8 proce

RE: [gmx-users] query regarding mk_angndx

ch 2013 2:09 AM > To: Discussion list for GROMACS users > Subject: [gmx-users] query regarding mk_angndx > > -- Forwarded message -- > From: Kavyashree M > Date: Fri, Mar 8, 2013 at 10:45 PM > Subject: query regarding mk_angndx > To: Discussion list for GROMA

[gmx-users] query regarding mk_angndx

-- Forwarded message -- From: Kavyashree M Date: Fri, Mar 8, 2013 at 10:45 PM Subject: query regarding mk_angndx To: Discussion list for GROMACS users Dear users, I used mkang_ndx to create an index file with dihedral angles. Input was: mk_angndx -s a.tpr -n angle.ndx -ty

[gmx-users] query regarding mk_angndx

Dear users, I used mkang_ndx to create an index file with dihedral angles. Input was: mk_angndx -s a.tpr -n angle.ndx -type dihedral output angle.ndx read like this - [ Phi=180.0_2_43.93 ] 52018192237353627323031 39595758

Re: [gmx-users] query for gromacs-4.5.4

On 3/6/13 4:20 AM, Chaitali Chandratre wrote: Dear Sir , I am new to this installation and setup area. I need some information for -stepout option for What more information do you need? mdrun_mpi and also probable causes for segmentation fault in gromacs-4.5.4. (my node having 64 GB mem r

[gmx-users] query for gromacs-4.5.4

Dear Sir , I am new to this installation and setup area. I need some information for -stepout option for mdrun_mpi and also probable causes for segmentation fault in gromacs-4.5.4. (my node having 64 GB mem running with 16 processes, nsteps = 2000) Thanks in advance. -- With Regards, Ch

Re: [gmx-users] Query on generate velocities and gen_temp in mdp files for REMD simulations

On 1/16/13 3:56 AM, Neha Gandhi wrote: Dear Help, I am trying to run REMD simulations and found couple of interesting discussions on GROMACS mailing list regarding ensembles which can be used during REMD. I will be running REMD of small peptide in explicit solvent and I am confused about gen_

[gmx-users] Query on generate velocities and gen_temp in mdp files for REMD simulations

Dear Help, I am trying to run REMD simulations and found couple of interesting discussions on GROMACS mailing list regarding ensembles which can be used during REMD. I will be running REMD of small peptide in explicit solvent and I am confused about gen_temp and gen_vel parameters for these simul

Re: [gmx-users] query regarding PMF calculation

On 11/29/12 11:55 AM, Timir Hajari wrote: Hi, I am trying to calculate PMF using pull code by freezing two pull groups as I need to calculate PMF for a particular orientation. Is it meaning to use pull code in this condition(freezing two pull groups) ?? I will wait for your helpful suggestions.

Re: [gmx-users] Query about GPU version of Gromacs

Hi, The GPU functionality available in GROMACS 4.5 based on OpenMM is likely to be deprecated because we lack the resources to continue to support it - as you can see from the limited documentation you can see for it on our website. I would advise against attempting to build or use anything other

[gmx-users] Query about GPU version of Gromacs

Hai all, Can any body suggest me which is most stable version of GPU-GROMCS. and as far as Gromacs site is concerned currently all the versions are unstable. If there is no stable version for GPU is available then when would a stable version for GPU would be released. and another query

Re: [gmx-users] query on table potential

On 8/06/2012 1:09 PM, Sanku M wrote: Hi, I am trying to use a table potential implementing Weeks-Chandler-Anderson (WCA) interaction between a solute and all atoms of a solvent like TIP3P water ( with nonzero interaction in the Hydrogen atoms) . But, I am having a trouble in specifying energ

[gmx-users] query on table potential

Hi,   I am trying to use a table potential implementing Weeks-Chandler-Anderson (WCA) interaction between a solute and all atoms of a solvent like TIP3P water ( with nonzero interaction in the Hydrogen atoms) . But, I am having a trouble in specifying energy groups required for table potential. 

Re: [gmx-users] query reg.

On 28/02/2012 3:36 PM, Vishwambhar Bhandare wrote: Hello, Is it possible to analyse structure during running simulation? Hw we can do that Make a copy of the trajectory file and then do whatever you want. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailma

[gmx-users] query reg.

Hello, Is it possible to analyse structure during running simulation? Hw we can do that Thanks and Regards, -- Vishwambhar Centre for Bioinformatics Pondicherry University Pondicherry -- Note: Strictly confidential to Vishwayogi -- gmx-users mailing

Re: [gmx-users] Query regarding energy minimization for packing the lipids around the protein

Anushree Tripathi wrote: I have used "mdrun -v deffnm em" command for energy minimization just after running the command i.e., given below: perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat But When I run the command which is given below: Eeee

Re: [gmx-users] Query regarding energy minimization for packing the lipids around the protein

On 25/01/2012 9:32 PM, Anushree Tripathi wrote: I have used "mdrun -v deffnm em" command for energy minimization just after running the command i.e., given below: perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat But When I run the command which is

[gmx-users] Query regarding energy minimization for packing the lipids around the protein

I have used "mdrun -v deffnm em" command for energy minimization just after running the command i.e., given below: perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat But When I run the command which is given below: Ek! No confout.gro at all! Died at inflategro.pl line 81.

Re: [gmx-users] query on g_sorient

Sanku M wrote: Hi, I am trying to understand what are the angles g_sorient plans to compute. The manual says that the theta1 is "the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3" . But, I wonder what is the reference position of

[gmx-users] query on g_sorient

Hi,   I am trying to understand what are the angles g_sorient plans to compute.  The manual says that the theta1 is "the angle with the vector from the first atom of the solvent molecule to the midpoint between atoms 2 and 3" .  But, I wonder what is the reference position of this angle  ? In ot

[gmx-users] query about identifying representative snapshots from a 2D FEL

Dear Gromacs users I am interested in identifying the representative snapshots from a 2D Free energy landscape plot generated using g_sham using the reaction coordinates obtained from EV1 and EV2 projections. Can some suggest on how to back trace the coordinates from a 2D FEL and also the t

[gmx-users] query on 1-4 interaction

Hi,    I have a question regarding how the 1-4 interaction works in GROMACS4.5.4 with charmm force field and its relation with number of exclusions ( nrexcl)  If we choose charmm forcefield ( or opls forcefield) in pdb2gmx, it writes down the topology file topol.top    with nrexcl 3 . If I try t

Re: [gmx-users] query regarding source of error

Hi Anushree, I assume the rudeness of the last two sentences is unintentional. You might benefit from reading http://catb.org/~esr/faqs/smart-questions.html The problem only occurs if you generated a topology by yourself or took it from someone else. That would indicate that you're a relatively a

[gmx-users] query regarding source of error

I m not getting the meaning of source of error mentioned in user i.e.,"charge groups encompass too many atoms. Most charge groups should be less than 4 atoms or less".Let me know the exact meaning of this source of error.Reply me soon. -- gmx-users mailing listgmx-users@gromacs.org http://lis

Re: [gmx-users] query on partial charge entry in topology

Sanku M wrote: Hi, I find that in the ffnonbonded.itp under OPLS forcefield ( inside opls.ff directory), for each particle-type, there is a partial charge assigned to it. However, again in the .rtp file, for each residue, under each charge group, each of the atom is assigned another parti

[gmx-users] query on partial charge entry in topology

Hi,   I find that in the ffnonbonded.itp under OPLS forcefield ( inside opls.ff directory), for each particle-type, there is a partial charge assigned to it. However, again in the .rtp file, for each residue, under each charge group, each of the atom is assigned  another partial charge assigned

Re: [gmx-users] query for energy minimization in solvent

On 18/11/2011 7:40 AM, Anushree Tripathi wrote: Yes I m using 4.0.7 version.so for that how could I change the name accordingly. You used it in your [molecules] section. Change it to what it should be, per ions.itp. Mark On Sat, Nov 5, 2011 at 1:37 AM, Justin A. Lemkul

Re: [gmx-users] query for energy minimization in solvent

Anushree Tripathi wrote: Yes I m using 4.0.7 version.so for that how could I change the name accordingly. Check ions.itp and use the names required by your chosen force field. -Justin On Sat, Nov 5, 2011 at 1:37 AM, Justin A. Lemkul > wrote: Anushree Tripat

Re: [gmx-users] query for energy minimization in solvent

Yes I m using 4.0.7 version.so for that how could I change the name accordingly. On Sat, Nov 5, 2011 at 1:37 AM, Justin A. Lemkul wrote: > > > Anushree Tripathi wrote: > >> when i run the given command i.e, >> >> grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr >> It is showing f

Re: [gmx-users] Query on restraining center of mass of a protein

On 15/11/2011 10:21 AM, Sanku M wrote: Hi, I have a system containing water and a large protein. In the simulation, I do not want the protein center of mass to drift away. Why do you want it not to drift away? There's nothing magical about the center of a periodic simulation cell. Why do yo

[gmx-users] Query on restraining center of mass of a protein

Hi,   I have a system containing water and a large protein. In the simulation, I do not want the protein center of mass to drift away. I was wondering what will be the reasonable method in gromacs to fix the position of the center of mass of the protein in its original position . I was thinking

Re: [gmx-users] query for energy minimization in solvent

Anushree Tripathi wrote: when i run the given command i.e, grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr It is showing fatal error:No such molecule type NA. How could I troubleshoot this problem? Ion naming is listed in ions.itp - the "NA" name works for all force fields

[gmx-users] query for energy minimization in solvent

when i run the given command i.e, grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr It is showing fatal error:No such molecule type NA. How could I troubleshoot this problem? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Plea

Re: [gmx-users] query on OPLS-2005

Hi Cara,    Thanks for a  very clarifying email. It helps a lot. Sanku From: Cara Kreck To: gmx-users@gromacs.org Sent: Friday, October 28, 2011 3:50 AM Subject: RE: [gmx-users] query on OPLS-2005 Hi Sanku According to the Schrodinger Knowledge Base, this

RE: [gmx-users] query on OPLS-2005

romacs.org Subject: [gmx-users] query on OPLS-2005 Hi, I wanted to check what is actually OPLS-2005 forcefield that is recently being referred often for md simulation. However, I also see that whenever, OPLS-2005 is being referred, it cites a 2001 paper by Jorgensen on OPLS forcefield. So, what i

[gmx-users] query on OPLS-2005

Hi,   I wanted to check what is actually OPLS-2005 forcefield that is recently being referred often for md simulation. However, I also see that whenever, OPLS-2005 is being referred, it cites a 2001 paper by Jorgensen on OPLS forcefield. So, what is actually OPLS-2005? So, I wonder what version

Re: [gmx-users] query on Free energy perturbation

Sanku M wrote: Hi, I was planning to use Thermodynamic integration to calculate solvation free energy of a molecule in a solvent. I was following Justin Lemkul's online tutorial. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html . I found t

[gmx-users] query on Free energy perturbation

Hi, I was planning to use Thermodynamic integration to calculate solvation free energy of a molecule in a solvent. I was following Justin Lemkul's online tutorial. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html . I found that a) a sd int

Re: [gmx-users] query regarding g_ras command

rashi parihar wrote: thanx justin..my problem is that i do not know exactly the syntax of command.i get to know about this command through this community only.i.e why i want the full command? Please read the contents of the manual about g_sas and/or g_sas -h for a full list of options (l

Re: [gmx-users] query regarding g_ras command

thanx justin..my problem is that i do not know exactly the syntax of command.i get to know about this command through this community only.i.e why i want the full command? On Tue, Jun 21, 2011 at 6:53 PM, Justin A. Lemkul wrote: > > > rashi parihar wrote: > >> I want to obtain solvent accessible

Re: [gmx-users] query regarding g_ras command

rashi parihar wrote: I want to obtain solvent accessible surface area using g_sas command: g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.plz tell me the full command as i am getting error while running this command.thanx in advance!! To get an answer you need to provide an actual command a

[gmx-users] query regarding g_ras command

I want to obtain solvent accessible surface area using g_sas command: g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.plz tell me the full command as i am getting error while running this command.thanx in advance!! how I will obtain three output files containing: area.xvg, resarea.xvg and atomarea.x

Re: [gmx-users] query regarding replica exchange

Often, a PBS submission system will provide the host information to MPI automatically. However, you will have to refer to the documentation for your particular cluster (or talk to the sysadmin, as Justin mentioned) to determine if your particular cluster behaves this way, which MPI process startup

Re: [gmx-users] query regarding replica exchange

Sanku M wrote: I was wondering if I try to run PBS script in a cluster, how can I get to generate the hostfile as I do not know in advance which machines will be allocated . This is a question for your sysadmin. Most such implementations ignore hostfiles for this very reason. -Justin

Re: [gmx-users] query regarding replica exchange

Subject: Re: [gmx-users] query regarding replica exchange On 26/05/2011 8:50 AM, Joshua L. Phillips wrote: > You will need a file formatted like the following: > > node0 slots=4 max_slots=4 > node1 slots=4 max_slots=4 > ... > node9 slots=4 max_slots=4 > > You will then need to use

Re: [gmx-users] query regarding replica exchange

On 26/05/2011 8:50 AM, Joshua L. Phillips wrote: You will need a file formatted like the following: node0 slots=4 max_slots=4 node1 slots=4 max_slots=4 ... node9 slots=4 max_slots=4 You will then need to use the -hostfile option to supply the filename to either mpiexec or mpirun (not mdrun).

Re: [gmx-users] query regarding replica exchange

You will need a file formatted like the following: node0 slots=4 max_slots=4 node1 slots=4 max_slots=4 ... node9 slots=4 max_slots=4 You will then need to use the -hostfile option to supply the filename to either mpiexec or mpirun (not mdrun). -- Josh On Wed, 2011-05-25 at 11:50 -0700, Sanku M

[gmx-users] query regarding replica exchange

Hi, I am planning to run replica exchange simulation using gromacs 4.0.7 . I have read the manual about REMD. Only thing I wanted to know is that how I can specify the name of host-machines where I am planning to run the simulations. I have 10 different quad-core computers each intra-connect

Re: [gmx-users] Query

On 4/23/2011 4:54 PM, NAGA MANI wrote: editconf -f conf.gro -o newbox.gro -c -d 1.0 -bt dodecahedron while typing this command i got error... Fatal error: Atom type CH3 not found... I think you were using a different command when you saw this error. If you copy and paste more of the context

[gmx-users] Query

editconf -f conf.gro -o newbox.gro -c -d 1.0 -bt dodecahedron while typing this command i got error... Fatal error: Atom type CH3 not found... -- S. NAGAMANI C/O Dr. M. Karthikeyan Department of Bioinformatics Alagappa University Karaikudi-630003. -- gmx-users mailing listgmx-users@gromacs

Re: [gmx-users] query against box collapsed in case of tightly bound ligand

devawati dutta wrote: Dear Sir, Thank you for your suggestion regarding coulomb type and LIE method. I have successfully done the job. But now I am facing another type of problem. I am performing simulation of a protein ligand complex where the ligand is si

[gmx-users] query against box collapsed in case of tightly bound ligand

Dear Sir, Thank you for your suggestion regarding coulomb type and LIE method. I have successfully done the job. But now I am facing another type of problem. I am performing simulation of a protein ligand complex where the ligand is sitting deep inside the grrove o

Re: [gmx-users] Query for RMSD

On 01/24/11, Archana Sonawani wrote: > Hello, > >   > > I have run 10 ns simulation for ligand-receptor complex. For analysis, I > checked RMSD, Radius of gyration, Hydrogen bonds and distance using g_dist. > >   > > In the RMSD plot, the whole simulation shows RMSD between 0 - 0.5nm , bu

[gmx-users] Query for RMSD

Hello, I have run 10 ns simulation for ligand-receptor complex. For analysis, I checked RMSD, Radius of gyration, Hydrogen bonds and distance using g_dist. In the RMSD plot, the whole simulation shows RMSD between 0 - 0.5nm , but after 5ns I get long vertical lines upto 2.5 nm. I dont know whats

Re: [gmx-users] query for binding energy

devawati dutta wrote: Dear Sir, I have simulated my protein ligand complex without using PME but with cut-off as coulombtype parameter. With g_energy command I am getting the value of non-bonded interactions as follows: Interaction LJ-SR LJ-LR Coul-SR

[gmx-users] query for binding energy

Dear Sir, I have simulated my protein ligand complex without using PME but with cut-off as coulombtype parameter. With g_energy command I am getting the value of non-bonded interactions as follows: Interaction LJ-SR LJ-LRCoul-SR Coul-LR P+L(bound) -113.2000 -8.1800 -

Re: [gmx-users] Query about use of coulombtype for LIE in gromacs

On 5/01/2011 7:55 PM, devawati dutta wrote: Dear Sir, Thanks for your prompt answer. In LIE method, if I will not use the PME for coulombtype, then what is suitable for it? In gromacs manual, there are several options under coulomb type.Which one I will select for coulombtype and

[gmx-users] Query about use of coulombtype for LIE in gromacs

Dear Sir, Thanks for your prompt answer. In LIE method, if I will not use the PME for coulombtype, then what is suitable for it? In gromacs manual, there are several options under coulomb type.Which one I will select for coulombtype and Vdwtype in .mdp file? Your's sincerely Devawati

Re: [gmx-users] query for protein-igand binding energy calculation using LIE and Gromacs simulation

On 5/01/2011 5:06 PM, devawati dutta wrote: Dear Sir, I am using Gromacs 3.3.2 version for molecular dynamics simulation of my protein-ligand complex. I want to calculate the free energy of binding through LIE method. While extracting the LJ and coulombic energy values using g_en

[gmx-users] query for protein-igand binding energy calculation using LIE and Gromacs simulation

Dear Sir, I am using Gromacs 3.3.2 version for molecular dynamics simulation of my protein-ligand complex. I want to calculate the free energy of binding through LIE method. While extracting the LJ and coulombic energy values using g_energy command,there are many options like LJ-14, L

[gmx-users] query on decomposing potential of mean force

Hi, I am studying Potential of mean force(PMF) of association of two peptides. I want to decompose the PMF into energy(enthalpy) and entropic terms. But, I have some queries on how to extract those contributions . I found, in literature, generally, people try to get the energy(enthalpy)

Re: [gmx-users] query regarding missing residues

t the answer is no. So, I will go for loop reconstruction and will then see what happens. Regards Thanks and Regards -- Sonali Dhindwal --- On Tue, 12/10/10, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] query regarding missing residues To: "Discussion list for GRO

Re: [gmx-users] query regarding missing residues

sonali dhindwal wrote: Hello Sir, I want to ask a question about missing residues, for which coordinates are not defined in the PDB file. I have this protein structure and in one of the loop there are some residues whose coordinates are not defined in the file. When I did pdb2gmx for prepari

Re: [gmx-users] query regarding missing residues

- Original Message - From: sonali dhindwal Date: Wednesday, October 13, 2010 1:44 Subject: [gmx-users] query regarding missing residues To: Discussion list for GROMACS users --- | > Hello Sir, > > I want to ask a quest

[gmx-users] query regarding missing residues

Hello Sir, I want to ask a question about missing residues, for which coordinates are not defined in the PDB file. I have this protein structure and in one of the loop there are some residues whose coordinates are not defined in the file. When I did pdb2gmx for preparing the topology, it joined

Re: [gmx-users] Query regarding protonation and deprotonation of some residues

ific residue number. > > Regards > -- > Sonali Dhindwal > > > --- On *Mon, 27/9/10, Itamar Kass * wrote: > > > From: Itamar Kass > Subject: Re: [gmx-users] Query regarding protonation and deprotonation of > some residues > To: "Discussion list for GROMACS

Re: [gmx-users] Query regarding protonation and deprotonation of some residues

: From: Itamar Kass Subject: Re: [gmx-users] Query regarding protonation and deprotonation of some residues To: "Discussion list for GROMACS users" Date: Monday, 27 September, 2010, 10:07 AM Hi, You need to define the protonation sate vie pdb2gmx. pdb2gmx

Re: [gmx-users] Query regarding protonation and deprotonation of some residues

Hi, You need to define the protonation sate vie pdb2gmx. pdb2gmx -tyr -lys On 27/09/10 2:34 PM, sonali dhindwal wrote: Hello All, I came through this research article, in which author has selectively deprotonated and protonated some of the residues to simulate the condition for electrostat

[gmx-users] Query regarding protonation and deprotonation of some residues

Hello All, I came through this research article, in which author has selectively deprotonated and protonated some of the residues to simulate the condition for electrostatic interaction with the substrate while carrying out molecular dynamics simulation. It will be appreciable, if you could help

Re: [gmx-users] Query: regarding how to include crystal water of pdb file as TIP4P water molecule

- Original Message - From: bipin.si...@research.iiit.ac.in Date: Sunday, August 1, 2010 17:15 Subject: [gmx-users] Query: regarding how to include crystal water of pdb file as TIP4P water molecule To: gmx-users@gromacs.org > Hi all, > > I am facing problem during the grompp s

Re: [gmx-users] Query: regarding how to include crystal water of pdb file as TIP4P water molecule

Dear Bipin, Why not just erase the water molecules from the crystal? You can do this before the pdb2gmx step and then, when you solvate the box with genbox you'll have only one type of water both in the gro and topology file. That's at least one way to deal with it. Regards, -Shay On Sun, Aug 1,

[gmx-users] Query: regarding how to include crystal water of pdb file as TIP4P water molecule

Hi all, I am facing problem during the grompp step as in the topology file the crystal water and solvent water molecules added during solvation of the box are being treated as two different solvent in gromacs and showing error that the Fatal error: number of coordinates in coordinate file (input.

[gmx-users] Query on WHAM analysis

loc_win_min is the center of restraint spring is the force constant in kcal/mol (1000kJ/mol/nm^2 /4.184 = x kcal/mol/nm^2) You should probably read the manual again, this stuff is all there. I'll not answer any further questions on this as (1) it's in Alan's manual, and (2) this list is not

[gmx-users] Query on WHAM analysis

Hi all, I am doing the umbrella sampling of a ligand pathway (Gromacs4.0.4).Now i want to plot the PMF using WHAM analysis by Alan Grossfield. I installed the WHAM program, read the manual too. But i am confused with the "loc_win_min" and "spring" terms in the metadata file. Can anyone please exp

Re: [gmx-users] Query regarding g_rmsf and g_hbond

Erik Marklund skrev: rituraj purohit skrev: Dear friends, I have some query regarding g_rmsf and g_hbond 1) Through g_rmsf we can plot rmsf Vs atom number (it is by default) but i want to plot rmsf Vs time, how i can do that? 2) Through g_hbond we can plot number of H-bonds Vs Time (By defau

Re: [gmx-users] Query regarding g_rmsf and g_hbond

rituraj purohit skrev: Dear friends, I have some query regarding g_rmsf and g_hbond 1) Through g_rmsf we can plot rmsf Vs atom number (it is by default) but i want to plot rmsf Vs time, how i can do that? 2) Through g_hbond we can plot number of H-bonds Vs Time (By default) but i want to plot

[gmx-users] Query regarding g_rmsf and g_hbond

Dear friends, I have some query regarding g_rmsf and g_hbond 1) Through g_rmsf we can plot rmsf Vs atom number (it is by default) but i want to plot rmsf Vs time, how i can do that? 2) Through g_hbond we can plot number of H-bonds Vs Time (By default) but i want to plot number of h-bonds Vs res

[gmx-users] query about generation of 2D histogram

Respected Sir,     I am trying to generate free energy landscape by using g_sham,From the archive I came to know that one .xvg file needs to be prepared containing three columns of data, first one is time, 2nd and 3rd one are the coordinates of interest, I used the command g_sham -f *.xvg -l

[gmx-users] query on constraint-force pull code

Hi, I would like to use constraint force pull code to calculate the free energy of association of two peptide using the distance between center of mass of two peptides as reaction coordinate. I am planning to use gromacs 4. Here I have some queries: 1. Since I will constraint method, I guess,

Re: [gmx-users] query regarding atom type

Thanks a lot for your mail. I hope it will help me. Regards -- Sonali Dhindwal --- On Sat, 27/3/10, dur...@zib.de wrote: From: dur...@zib.de Subject: Re: [gmx-users] query regarding atom type To: "Discussion list for GROMACS users" Date: Saturday, 27 March, 2010, 8:56 PM hi t

Re: [gmx-users] query regarding atom type

hi there, i'm doing simulation of protein-ligand systems since a few weeks and i've been starting with a nice tutorial for acpypi (python script) http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs in order to create topology-files for several (42) ligands in an automized way. works very

Re: [gmx-users] query regarding atom type

emkul //* wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] query regarding atom type To: "Discussion list for GROMACS users" Date: Saturday, 27 March, 2010, 8:14 PM sonali dhindwal wrote: > Hello All > I am trying to add ions to my protein, for

Re: [gmx-users] query regarding atom type

: Re: [gmx-users] query regarding atom type To: "Discussion list for GROMACS users" Date: Saturday, 27 March, 2010, 8:14 PM sonali dhindwal wrote: > Hello All > I am trying to add ions to my protein, for that I have run this command,, > > [sak...@localhost ~/sonali]$

Re: [gmx-users] query regarding atom type

sonali dhindwal wrote: Hello All I am trying to add ions to my protein, for that I have run this command,, [sak...@localhost ~/sonali]$ grompp -f ions.mdp -c protein_solv.gro -p topol.top -o ions.tpr and every time I run it, following error is coming Fatal error: Atomtype OA not found I am

[gmx-users] query regarding atom type

Hello All I am trying to add ions to my protein, for that I have run this command,, [sak...@localhost ~/sonali]$ grompp -f ions.mdp -c protein_solv.gro -p topol.top -o ions.tpr and every time I run it, following error is coming Fatal error: Atomtype OA not found I am using OPLSA force field and

Re: [gmx-users] query regarding neutralisation of charge on protein

sonali dhindwal wrote: Hello All, I am trying to do MD on my modelled protein and when I ran pdb2gmx command, it is showing that Total charge -12.000 e now I read in the tutorial that when there is a total charge, then we have to neutralise that charge by adding ions, but in my case it is i

[gmx-users] query regarding neutralisation of charge on protein

Hello All, I am trying to do MD on my modelled protein and when I ran pdb2gmx command, it is showing that Total charge -12.000 e now I read in the tutorial that when there is a total charge, then we have to neutralise that charge by adding ions, but in my case it is in negative (what the output

Re: [gmx-users] Query regarding toplogy of Manganese ion in protein

could easily be too large in scope for someone without years of MD experience. Mark --- On *Wed, 24/3/10, Justin A. Lemkul //* wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] Query regarding toplogy of Manganese ion in protein To: "Discussion list for GROMACS

Re: [gmx-users] Query regarding toplogy of Manganese ion in protein

Thanks for your help I hope it will work. Regards -- Sonali Dhindwal --- On Wed, 24/3/10, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] Query regarding toplogy of Manganese ion in protein To: "Discussion list for GROMACS users" Date: Wednesday, 24 March,

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