Re: [gmx-users] velocity was not present from trjconv

On 2/12/13 9:17 AM, Albert wrote: Hello: I am using Gromacs4.6 and I extract one of my frame into .gro file by command: trjconv_mpi -f md.xtc -s md.tpr -dump 25000 -o md.gro I found that the velocity information was not present in this 25ns-md.gro file: Velocities are not stored in .xtc

Re: [gmx-users] velocity was not present from trjconv

On 2/12/13 9:25 AM, Albert wrote: On 02/12/2013 03:19 PM, Justin Lemkul wrote: Velocities are not stored in .xtc files. They are stored in .trr files, if nstvout != 0 in the .mdp file. -Justin Hi Justin: thanks for kind comments. I used the following settings and I didn't gen

Re: [gmx-users] velocity was not present from trjconv

On 2/12/13 9:32 AM, Albert wrote: On 02/12/2013 03:28 PM, Justin Lemkul wrote: Extract it from the .cpt file that corresponds to that frame. -Justin thanks a lot for such helpful comments. I found that the md production produced two .cpt file: state.cpt state_prev.cpt I am not sure

Re: [gmx-users] can we schedule it?

On 2/12/13 9:45 AM, Albert wrote: Hello: I've got a question for setting of .mdp file for MD productions. The .trr file is really huge if we are going to run longer MD simulations. In this case, I usually only consider generate .xtc file, but the velocity is missed for all steps except the l

Re: [gmx-users] different springs - WHAM

On 2/12/13 9:40 AM, Steven Neumann wrote: Dear Gmx Users, I know it is possible to combine windows with different spring constants into the one PMF curve using g_wham. Do I have to somehow tell g_wham that one or two windows have different spring constants? No, they are read from the .tpr

Re: [gmx-users] Intra-protein hydrophobic contacts

On 2/12/13 11:29 AM, Kavyashree M wrote: Dear Users, How can intra-protein hydrophobic contacts be found for a trajectory. Most of the mails regarding this in the list is regarding hydrophobic contacts between chains or ligand and protein. So kindly help. Create a group of hydrophobic atoms

Re: [gmx-users] Re: what do Coul-SR, LJ-SR, Coul-14 and LJ-14 mean in g_energy

On 2/12/13 11:06 AM, escajarro wrote: Hello all, I am afraid that, after reading all the documentation I could find about Coul-SR and LJ-SR, I still do not understand what these terms account for. I am running a simulation of one single polymer chain in water. My values for cut-off radious ar

Re: [gmx-users] different springs - WHAM

On 2/12/13 9:57 AM, Steven Neumann wrote: On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul wrote: On 2/12/13 9:40 AM, Steven Neumann wrote: Dear Gmx Users, I know it is possible to combine windows with different spring constants into the one PMF curve using g_wham. Do I have to somehow

Re: [gmx-users] error in md.log files

On 2/12/13 10:29 AM, vidhya sankar wrote: Dear Justin Thank you for your reply, I have set the Restraint Along the Z Axis . as follows #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] i funct fcxfcyfcz 1

Re: [gmx-users] Error: The Y-size of the box times the triclinic skew factor is smaller than the number of DD cells times the smallest allowed cell size

On 2/12/13 5:24 PM, Sonia Aguilera wrote: Hi, I was performing a NPT calculation, and I got this error: The Y-size of the box (6.002812) times the triclinic skew factor (1.00) is smaller than the number of DD cells (6) times the smallest allowed cell size (1.000605) I also tried to chang

Re: [gmx-users] Re: Error: The Y-size of the box times the triclinic skew factor is smaller than the number of DD cells times the smallest allowed cell size

On 2/12/13 5:44 PM, Sonia Aguilera wrote: Thank you Justin, So, your advice is not to perform the npt calculation and to run the md after the nvt? A common mistake is to think that there is a "standard" protocol that one must follow. While it is true that for the condensed phase, a common

Re: [gmx-users] installation

On 2/12/13 9:24 PM, David Sáez wrote: Hello everybody, I'm trying to install Gromacs 4.6 in my Ubuntu 12.04 laptop. As I am not a a skilled user, I tried the Quick and Dirty Installation, After following the instructions I obtained this message when trying to execute GMXRC: david@HAL-9000:~$ /

Re: [gmx-users] Regarding pH simulation

On 2/13/13 8:23 AM, Sathish Kumar wrote: Hai, I want to do simulation of a protein at pH 12.but I was unable to do that and I dont know how to set up mdp files for the pH.Can you please suggest me how to do. thank You. This question gets asked prett

Re: [gmx-users] md with multiple ligands

On 2/13/13 5:24 AM, Ansuman Biswas wrote: Dear gromacs users, I wish to run a protein ligand md in Gromacs 4.5.3 with charmm force field. Its a dimeric protein with a MG ion and 2 ligands bound to two active sites. I wish to run the dimer and there would be 4 ligands. I generated the topology

Re: [gmx-users] Stopping protein jumping inside box

On 2/13/13 8:47 AM, Naga Sundar wrote: Hi Plz try -pbc nojump option...It may work Several iterations of trjconv are often needed to achieve the desired representation. Indeed, the first step to removing jumps should be -pbc nojump...which removes jumps ;) -Justin On Wed, Feb 1

Re: [gmx-users] different springs - WHAM

On 2/13/13 5:23 PM, Steven Neumann wrote: On Tue, Feb 12, 2013 at 5:01 PM, Justin Lemkul wrote: On 2/12/13 9:57 AM, Steven Neumann wrote: On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul wrote: On 2/12/13 9:40 AM, Steven Neumann wrote: Dear Gmx Users, I know it is possible to

Re: [gmx-users] Implicit solvent

On 2/14/13 1:01 AM, Алексей Раевский wrote: Hi, dear developers! I want to ask you abou dynamics in implicit solvent. I have a complex of animal protein - dimer/trimer. After modeling by homology I have built another one from the plant organism. Dimer/trimer was constructed with superposition

Re: [gmx-users] md with multiple ligands

-- Message: 8 Date: Wed, 13 Feb 2013 08:28:00 -0500 From: Justin Lemkul Subject: Re: [gmx-users] md with multiple ligands To: Discussion list for GROMACS users Message-ID: <511b94e0.4040...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1;

Re: [gmx-users] Distance restraints

On 2/14/13 8:35 AM, Divya Sunil wrote: Hello all, I have been trying to apply distance restraints on my protein. I prepared distance restrains using make index and added to topology file. I did it just after executing pdb2gmx. Is this the correct procedure to apply distance restraints? make

Re: [gmx-users] installation

On 2/14/13 9:40 AM, David Sáez wrote: Erik, thanks for your answer. I typed "which mdrun" and I got this output: *~$ which mdrun* */usr/local/gromacs/bin/mdrun* Then, I typed just "mdrun" and I got this: *~$ mdrun* * * * :-) G R O M A C S (-:* * * *

Re: [gmx-users] Implicit solvent

On 2/14/13 10:21 AM, Sebastien Cote wrote: Dear Justin, I am not sure to follow you. You essentially say that it is better to avoid using implicit solvent i.e. the generalized Born-formalism implemented in GROMACS? For the case of optimizing and relaxing a system (expecting short MD), I agre

Re: [gmx-users] Implicit solvent

On 2/14/13 11:02 AM, Sebastien Cote wrote: Dear Justin, Thank you very much for your answer. I did not take this as a criticism of implicit solvent model. I was just wondering what was the origin of the limitations you were speaking of. I did some small implicit solvent simulations, but I mus

Re: [gmx-users] RE:Stopping protein jumping inside box?

Please don't reply to the entire digest. Copy and paste relevant portions and omit the rest. On 2/14/13 11:54 AM, 라지브간디 wrote: I have tried -pbc nojump, and other options given in that link but still my protein gets jumped! Plz guide me, how to stop this ? The suggested trjconv workflow

Re: [gmx-users] Removing errors related to missing dihedrals.

On 2/14/13 11:54 AM, Abhishek Acharya wrote: Hello Justin Thank you very much for your effort and help. I will try adding new parameter corresponding to the errors. Meanwhile just out of curiosity and possible need, what should be done in case no matching parameters are found for the missing di

Re: [gmx-users] Removing errors related to missing dihedrals.

On 2/14/13 4:15 PM, Abhishek Acharya wrote: Hello Justin Thank you very much for your effort and help. I will try adding new parameter corresponding to the errors. Meanwhile just out of curiosity and possible need, what should be done in case no matching parameters are found for the missing

Re: [gmx-users] General query regarding MD simulation.

On 2/15/13 1:29 PM, Abhishek Acharya wrote: Dear GROMACS Users. Just out of curiosity, i would like to pose a general question here ( i didn't have an idea of any other suitable forum ). My protein active site has a GDP which is coordinated to a Mg ion. The Mg ion itself coordinates two water

Re: [gmx-users] Extracting the last frame of simulation into PDB

On 2/15/13 2:08 PM, zugunder wrote: Hi, I bumped into a small problem, I think I missed something... so I am asking for help. I made a simulation of a protein in water (35ns, extended 3 times from initial 10ns) and now I need to get a resulting protein structure in pdb. So I issued: g_trjcon

Re: [gmx-users] Re: Extracting the last frame of simulation into PDB

On 2/15/13 3:22 PM, zugunder wrote: Oh, forgot about it completely... Thank you very much! BTW, is there any automated way to get rid of solvent molecules in PDB? I just need the structure for further manipulations (like mutations and adding several residues to the end). I do not find any opti

Re: [gmx-users] Changing the non-bonded interaction and charges?

On 2/15/13 4:20 PM, 라지브간디 wrote: Where can I change the particular Ligand atom ( can be C, O and N...etc) non-bonded interaction value and charges ? In its topology. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry

Re: [gmx-users] General query regarding MD simulation.

On 2/15/13 4:00 PM, Abhishek Acharya wrote: On 2/15/13 1:29 PM, Abhishek Acharya wrote: Dear GROMACS Users. Just out of curiosity, i would like to pose a general question here ( i didn't have an idea of any other suitable forum ). My protein active site has a GDP which is coordinated to a

Re: [gmx-users] Fw:some waters in active site of receptor

On 2/16/13 8:37 PM, aixintiankong wrote: Forwarding messages From: aixintiankong Date: 2013-02-16 23:54:51 To: gmx-users@gromacs.org Subject: some waters in active site of receptor Dear, there are three waters in active site of receptor, mediating the binding

Re: [gmx-users] Can not open file: traj.xtc

On 2/17/13 8:36 AM, Sabrina Kemmerer wrote: Hi Linus, sorry, I did not mention that. Yes, I tried it with the -f parameter set and without. In both cases I get the same error. Please provide us with the exact command line you used (copied and pasted directly from the terminal) as well as t

Re: [gmx-users] Can not open file: traj.xtc

On 2/17/13 10:11 AM, Sabrina Kemmerer wrote: Hi, the 'ls -lh' output is -rw-r--r-- 1 sabrina sabrina 32 Feb 11 19:49 c8vectors.ndx -rw-rw-r-- 1 sabrina sabrina 7.8M Jan 19 18:54 confout.gro -rw-r--r-- 1 sabrina sabrina 33 Feb 11 19:49 labelvektors.ndx -rw-r--r-- 1 sabrina sabrina 33 Feb

Re: [gmx-users] Protein in GdmCl solution

On 2/18/13 6:29 AM, Biswajit Gorai wrote: Dear GMX Users, Past few months I am struggling to unfold my protein using Guanidinium (GDM) solutions (3,4,5,6 M). I already did temperature (upto 498 K) induced unfolding, and able to get expected results in 60 ns. For GDM (6M), I did simulation upto

Re: [gmx-users] Protein in GdmCl solution

On 2/18/13 9:54 AM, Biswajit Gorai wrote: Dear Justin, Thanks a lot for your reply. As u mentioned, I edited the mass as follows: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBch argeB 1 CA 1GDM C1 10.99610 12.010

Re: [gmx-users] md with multiple ligands

-- Message: 8 Date: Wed, 13 Feb 2013 08:28:00 -0500 From: Justin Lemkul <[hidden email]> Subject: Re: [gmx-users] md with multiple ligands To: Discussion list for GROMACS users <[hidden email]> Message-ID: <[hidden email]> Content-Type: text/plain;

Re: [gmx-users] Re: A note while running grompp for nvt equilibration

On 2/19/13 1:36 AM, Anu Chandran wrote: Sir, Thank you for the reply. As per the suggestion, I tried increasing the rlist. Note or warning stopped when rlist was increased to 1.8. Also with this value of rcoulomb, the box size also needs to be increased. I would like to know whether it is fine

Re: [gmx-users] rtp topology file for ligand

On 2/19/13 4:23 AM, amna khan wrote: hi all, i generated the .itp file for my ligand using ATB, and i have generated the protein topology file by using the forcefield 13 my question is i need to generate the *ligand .top and .gro files* and when i use the command *pdb2gmx -f lig.pdb -o

Re: [gmx-users] There was 1 error in input file(s)

On 2/19/13 4:29 AM, 라지브간디 wrote: Dear GMX users, I have done nvt part and then start to do npt part for my protein but it shows error like Fatal error: There was 1 error in input file(s) Please how can avoid this? Fix the error :) In seriousness, no one can help you unless you provid

Re: [gmx-users] error in editconf

On 2/19/13 4:53 AM, az kalsom wrote: hi all, i generated the ligand topology file by prodrg server and then i generated the .out file from gaussain software aund used itp adjuster to adjsut the charges in ligand itp file but still i am getting the bad box error when i run the editconf command

Re: [gmx-users] NVT and NPT Equalibration

On 2/19/13 10:07 AM, Sainitin Donakonda wrote: Hi all, I want simulate my protein ligand complex for 20 nanoseconds..(final production run) So i set up NVT and NPT equlibrations for 200 ps each.. Can anyone tell me is this correct ? to setup 200 ps prior to 20 ns MD production? There is n

Re: [gmx-users] Ethanolamine force-field parameters missing in charmm27.ff

On 2/19/13 9:41 AM, jneeraj wrote: Hello, I plan to run a MD on a protein + ethanolamine (ETAM) system using Gromacs ver 4.5.5 with charmm27 force-field. Though charmm27 force-field (top_all27_prot_lipid.inp, also see http://users.mccammon.ucsd.edu/~rlaw/top_all27_prot_lipid.inp.htm

Re: [gmx-users] comm-grps

On 2/19/13 9:25 AM, fciocco wrote: Hi I want to study the interaction between a peptide and a lipid bilayer, with the peptide initialy outside de bilayer. Is correct to choose only "bilayer" and "SOL_ions" as comm-groups ? because grompp complain about that with a warning: some atoms are not

Re: [gmx-users] rtp topology file for ligand

s a system topology, encompassing all elements of the system and thus there can only be one. Other molecules (like your ligand) are #included in the system .top file using .itp format. -Justin On Tue, Feb 19, 2013 at 5:58 PM, Justin Lemkul wrote: On 2/19/13 4:23 AM, amna khan wrote: hi

Re: [gmx-users] Dihedral angel

On 2/19/13 10:52 AM, 라지브간디 wrote: I want to calculate the dihedral angel of side chain of Arginine. could you tell how it can be done? how do i create ndx for Arg and look at the dihedral angel in sinumation time point ? g_angle will measure the dihedral. Refer to g_angle -h for available

Re: [gmx-users] rtp topology file for ligand

On 2/19/13 12:53 PM, amna khan wrote: i generated the ligand.gro by using the command *editconf -g my_otp_ligand.pdb -o ligand.gro* * * *WARNING: all CONECT records are ignored* *Read 38 atoms* *No velocities found* it printed this and after this i did as mention in tutorial it generated the

Re: [gmx-users] trjconv woes (broken molecules)

On 2/19/13 1:28 PM, Ignacio Fernández Galván wrote: Hi all, I have a simulation with a frozen molecule which stays around the origin, and a number of solvent molecules with pbc. Due to the way the simulation cell is defined, with a corner at the origin, by default my frozen molecule appears

Re: [gmx-users] ATP all-atom FF in GROMACS (CHARMM36?)

On 2/19/13 1:29 PM, Bryan Roessler wrote: Hello, I am trying to locate an all-atom FF for ATP that I can use in GROMACS. The ATP residue is stored in a toppar stream file in CHARMM, thus it is not included in the download on the user-submission page for FFs. It also appears that it is not avai

Re: [gmx-users] NO velocities for ligand

On 2/19/13 2:39 PM, amna khan wrote: hello sir, i want to ask you i have GNERATED the ligand topolagy file by ATB and converting the optimized pdb to gro by editconf, it doesnot generated the volecities for ligand , why is this ? Because editconf has no business generating velocities. V

Re: [gmx-users] Problem with g_rdf

On 2/19/13 3:10 PM, Thomas Schlesier wrote: Dear all, I have a question regarding g_rdf. My system consits of 10 disacchardids (in the following A-B, with A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine the RDF (with flag '-rdf mol_com')for A-A, B-B and the intermolekular

Re: [gmx-users] Is it possible to use a force filed for Au?

On 2/19/13 4:57 PM, Ali Alizadeh wrote: Dear All users There are a wall(a gold crystal with 111 orientation) and a bulk of fluid(alkane) in my simulation box, My problem is, Is it possible to use a force filed for Au? Beside, Can I use two force field at the same time? You need a self-con

Re: [gmx-users] Problem with g_rdf

On 2/19/13 5:04 PM, Thomas Schlesier wrote: On 2/19/13 3:10 PM, Thomas Schlesier wrote: > Dear all, > I have a question regarding g_rdf. > My system consits of 10 disacchardids (in the following A-B, with > A-ring/monosaccharid and B-ring/monosaccharid) and i want to determine the RDF > (

Re: [gmx-users] Is it possible to use a force filed for Au?

On 2/19/13 5:07 PM, Ali Alizadeh wrote: Dear Justin Thank you for your reply, On 2/19/13 4:57 PM, Ali Alizadeh wrote: Dear All users There are a wall(a gold crystal with 111 orientation) and a bulk of fluid(alkane) in my simulation box, My problem is, Is it possible to use a force file

Re: [gmx-users] ngmx (was: Problem with g_rdf)

On 2/20/13 12:46 AM, Hector Manuel Manzanilla Granados wrote: Excuseme dear Dr. Tomas, forgiveme the boldness, I'm new with this, and I dont know who to address when I have a problem. My name is Hector, and I'm tryng to install the gromacs software in my computer; I follewed all the steps in t

Re: [gmx-users] Compare two bilayers made from two methods

On 2/20/13 4:09 AM, Kieu Thu Nguyen wrote: Dear all, I do not know whether there is any difference between a big bilayer and the other bilayer made from merging two small bilayers made before. I make a bilayer from two methods: (1) merging two small bilayers (made before) by the below comman

Re: [gmx-users] Distance for window spacing in US?

On 2/20/13 1:14 AM, Yun Shi wrote: Hi all, For the purpose of calculating deltaG from umbrella sampling, I have first pulled my ligand away from the enzyme active site along an arbitrary direction (say x axis), setting the enzyme as pull_group0. But I found the ligand was moving in the yz pla

Re: [gmx-users] About Restraint -NPT Equlibration

On 2/20/13 9:03 AM, vidhya sankar wrote: Dear Justin, Thank you for your Previous reply. I am DoingProtein- Lipid Simulation For My Assembly Of Cyclic Peptide As you Told Me I Have Used The Restraint on water oxygen Atom Along the Z-direction for My NVT equilibr

Re: [gmx-users] virtual sites in reference structure

On 2/20/13 9:18 AM, Ahmet yıldırım wrote: Dear users, I have the virtual sites in reference structure and all trajectory. When analyzing simulation, do I have to get rid of those(virtual sites)? If yes/no, why? Why do you think you need to remove them? -Justin -- =

Re: [gmx-users] the meaning of the dummy atom

On 2/20/13 9:20 AM, Ahmet yıldırım wrote: Dear users, What is the meaning of the dummy atom in Gromacs? Old terminology for virtual site. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA

Re: [gmx-users] g_order for lipid bilayers

On 2/20/13 9:41 AM, Felipe Pineda, PhD wrote: Hi, is it possible to apply g_order to a trajectory of a lipid bilayer when the carbon atoms of the acyl chains of the lipid molecules for which the SCD should be calculated are not numbered consecutively, i.e. the atom numbers corresponding to C21

Re: [gmx-users] pds files without bond information

On 2/20/13 1:59 PM, cdo wrote: Hi all, I'm new to Gromacs with a very basic question while I was reading tutorials. Tried to search this but I couldn't narrow down to useful discussions so far. It's simple. I saw some pdb files in the Tutorias. (such as LYSOZYME). But this particular pdb file

Re: [gmx-users] Distance for window spacing in US?

On 2/20/13 11:01 AM, Yun Shi wrote: Hi Justin, I was not able to find relevant posts in the archive. Any special keyword for searching? I'm afraid I can't think of anything magical off the top of my head, no. But I wonder if it would introduce any additional error to deltaG calculations

Re: [gmx-users] g_order for lipid bilayers

On 2/20/13 10:31 AM, Felipe Pineda, PhD wrote: Hi again, my topology is non-consecutively numbered. I was looking for a tool to renumber it, but didn't find it yet. A hint will be really appreciated. I was not sure I doubt one exists. Many people have asked for such a thing, but no one has

Re: [gmx-users] About Restraint on Water During NPT

On 2/20/13 10:30 AM, vidhya sankar wrote: Thank you justin for your Nice reply As you Mailed Me How Could i Check My System Is constructed efficiently or Poorly? Can I Check Through APL? I Have Stopped EM After Reaching APL as follows

Re: [gmx-users] some waters in active site of receptor

On 2/21/13 12:00 AM, aixintiankong wrote: Dear, there are three waters in active site of receptor,mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the sy

Re: [gmx-users] MDP settings for No Temperature Coupling

On 2/21/13 12:33 AM, bipin singh wrote: Hello All, I want to know how to mention a group (group2) without any temperature coupling in mdp file. From the manual I got to know that we should mention tau_t= -1 for no temperature coupling. And in the ref_temp section I have mention two values, 300

Re: [gmx-users] Extracting the timestep value from topology and/or trajectory files

On 2/21/13 9:47 AM, shavit wrote: Hello, For several months now, I've been writing my own analysis tools using the GROMACS template.c file. There is one thing I haven't been able to figure out, and that is how to get the timestep size. I'm confident this parameter is located in either the tr

Re: [gmx-users] MD simulation of protein-protein complex

On 2/21/13 10:18 AM, shahid nayeem wrote: Dear all I want to simulate a protein complex with 4 chains two of which is linked with disulfide bonds. Does this simulation requires that all chains are merged into one molecule definition or I should merge only two chains which are linked with disulf

Re: [gmx-users] position restrain of DNA

On 2/21/13 6:09 PM, Mehdi Bagherpour wrote: I am using Gromacs software for DNA simulation. Specially in my project I need to fix two ends base pairs of DNA,The DNA that I want to simulate has 12 sequence shown bellow 5-- *C*GCAACG*C* --3 3-- *G*CGTTGC*G* --5 I dont know how I can us

Re: [gmx-users] System size and minimum image convention

On 2/21/13 6:10 PM, Elisabeth wrote: Hello everyone, Does anyone know if the minimum image convention has something to do with the box size effect (independence of simulation results from system size) ? i.e. When the box size is larger than 2*r_c, does this ensure that the results are independ

Re: [gmx-users] Distance for window spacing in US?

On 2/21/13 6:24 PM, Yun Shi wrote: So in umbrella sampling, does it really matter if the vector connecting the COMs of protein and ligand is NOT parallel with the vector of the pulling force (although the pull rate is 0)? I guess as long as the force in each sampling window is along the same d

Re: [gmx-users] System size and minimum image convention

On 2/21/13 6:30 PM, Elisabeth wrote: Thanks Justin. Can you please elaborate on why for a binary (solute+solvent) the size should be larger than 2 Rc? I thought minimum image convention works for all atoms (solute ans solvent) and this makes sure forces are not double-counted. What if the solut

Re: [gmx-users] Statistical uncertainty in gromacs

On 2/21/13 6:58 PM, Juliette N. wrote: Hi Matthew, Thanks for your reply. I tried g_analyze as you suggested: 1) I am wondering why the average given by g_energy and g_analyze are not identical. I tried the following: g_energy -f Potential. edr -o Potential.xvg and extracted the average the

Re: [gmx-users] position restrain of DNA

corresponding [moleculetype]. -Justin On Fri, Feb 22, 2013 at 2:41 AM, Justin Lemkul wrote: On 2/21/13 6:09 PM, Mehdi Bagherpour wrote: I am using Gromacs software for DNA simulation. Specially in my project I need to fix two ends base pairs of DNA,The DNA that I want to simulate has 12

Re: [gmx-users] Statistical uncertainty in gromacs

nly output values every nstenergy frames for obvious reasons. -Justin Please help! Sorry for naive questions! On 21 February 2013 19:23, Justin Lemkul wrote: On 2/21/13 6:58 PM, Juliette N. wrote: Hi Matthew, Thanks for your reply. I tried g_analyze as you suggested: 1) I am wonderi

Re: [gmx-users] Energy minimization

On 2/21/13 9:10 PM, Kieu Thu Nguyen wrote: Dear all, I can not distinguish when the Fmax < 10 kJmol-1nm-1, < 100, < 1000 ? is appropriate Can anyone tell me which value is appropriate for lipid membrane, for protein in water, for protein in lipid membrane ? There is no absolute rule. Th

Re: [gmx-users] position restrain of DNA

topology, that approach will not use your special restraint file. -Justin On Fri, Feb 22, 2013 at 4:13 AM, Justin Lemkul wrote: On 2/21/13 7:35 PM, Mehdi Bagherpour wrote: Thanks Justin I have any question? i will use minimization with this restrain. using genrestr I make min.itp. h

[gmx-users] Re: [gmx-developers] Meaning of the -correct switch in g_potential

Please post usage questions to gmx-users. The gmx-developers list is for discussions on code modifications, bugs, and future directions of Gromacs. I am CC'ing gmx-users on this reply; please keep the discussion there. On 2/23/13 5:02 PM, Andrew DeYoung wrote: Dear Developers, I am very s

Re: [gmx-users] coordination number per residue

On 2/24/13 12:53 PM, benrezkallah djamila wrote: Hello everybody, I am working on a system consisting of protein-ions in water box. I need to calculate the coordination number per residue for my protein, I have searched the gmx mailing list, and, I have not find the solution. please, can you

Re: [gmx-users] Error during npt equilibration in coarse grained simulation

On 2/25/13 12:16 AM, Anu Chandran wrote: Dear users, I am trying to do a coarse grained simulation of an octamer of a 350 residue protein in water using gromacs-4.5.3 using martini force field. I got the following error when i started running NPT equilibration "Step 32, time 0.64 (ps) LINCS W

Re: [gmx-users] Simulation problem

On 2/25/13 1:01 AM, Jernej Zidar wrote: Hi. I've been running some polymer simulations on our cluster and I'm getting this error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. What does this error

Re: [gmx-users] request

On 2/25/13 6:09 AM, Group Gro wrote: Dear Gromacs Users. I apologize for asking a question that has come up several times by numerous users in the previous e-mails, but I have read the answers and suggestions to those posts and I am not still able to solve the problem based on them. It i

[gmx-users] Re: Dimer Dissociation Problem

Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. I am CC'ing the list and ask that further comments and questions will be posted there. On 2/25/13 7:42 AM, mrda...@gmail.com wrote: Dear Justin Greetings I simulate HIV-1 Protease with its subst

[gmx-users] Re: Regarding Gromacs error

Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. I am CC'ing the list and ask that further comments and questions will be posted there. On 2/25/13 9:09 AM, bhavaniprasad vipperla wrote: Hello sir, I have been using GROMACS for my MD work. I ha

Re: [gmx-users] Output for rmsd and radius of gyration doubts

On 2/25/13 9:38 PM, Ewaru wrote: Hi, Just need some advice regarding the following results I obtained while following the tutorial from this site, using a protein structure that I modelled using Modeller. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ 1. My

Re: [gmx-users] gbsa.itp for amber ff

On 2/25/13 10:05 PM, Yun Shi wrote: Hi all, If I want do MD simulation with amber ff and implicit solvent, would including gbsa.itp in .top file and specifying parameters in .mdp as follows be sufficient? implicit_solvent = GBSA gb_algorithm = OBC nstgbradii = 1.0 rgbradii =

Re: [gmx-users] Error during npt equilibration in coarse grained simulation

, of crashes with CG force fields during equilibration (hint: check the archives). You probably need either better minimization or a shorter time step. -Justin On Mon, Feb 25, 2013 at 6:58 PM, Justin Lemkul wrote: On 2/25/13 12:16 AM, Anu Chandran wrote: Dear users, I am trying to do a

Re: [gmx-users] Why not PBC for implicit solvent?

On 2/25/13 10:30 PM, Yun Shi wrote: Hi everyone, Previous posts mentioned setting pbc = none for MD simulations with implicit solvent. But I am trying to see the behavior of certain concentration of ligands (small molecules, no big biomolecules) in solvent, so I wonder if setting pbc = xyz wou

Re: [gmx-users] lennard jones 6-12 value setting

On 2/26/13 4:33 AM, 라지브간디 wrote: Dear gmx, I want set the particular value of lennard jones 6-12 for NO ligand for my simulation. I believe it has be mentioned in topology file created by force field. My questions is how to set these value in topology which created by CHARMM 27 ff? The d

Re: [gmx-users] help

On 2/26/13 7:46 AM, Sjøli Stian wrote: dear gmx-users, this is a stupid question (and partially a test of use). I cant find any information on how to use/modify maxvarn as a parameter for grompp. Can you point to examples or literature? Consider the help text: -maxwarn int0

Re: [gmx-users] request

se topics are discussed routinely. -Justin Thanks alot. ali kazemi department of biochemistry islamic azad university shahrekord branch -------- *From:* Justin Lemkul *To:* Group Gro ; Discussion list for GROMACS users *Sent:

[gmx-users] Re: genion

For the fourth time in two days, I'll start with: Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. I am CC'ing the list and ask that further comments and questions be posted there. On 2/26/13 9:03 AM, Samadashvili Nino wrote: Dear Justin,

Re: [gmx-users] Why not PBC for implicit solvent?

On 2/26/13 9:23 AM, Sebastien Cote wrote: Dear Justin (and Yun), Since our last discussion on implicit solvent simulations, I have read a bit more about how cutoffs in GBSA (or variants) implicit solvent simulations are used in other softwares such as AMBER, CHARMM and NAMD. It appears to me

Re: [gmx-users] About intial DPPC Pdb

On 2/26/13 11:01 AM, vidhya sankar wrote: Dear justin Thank you for your Previous Reply I am Doing Lipid Protein Simulation . As stated in your Website for Protein Lipid Tutorial I have Downloaded DPPC.pdb . and Did simulation As per Procedure ? My Question is Instead of Taking DP

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

On 2/26/13 11:30 AM, francesco oteri wrote: Dear gromacs users, in Bjelkmar et al. (2010) where the implementation of CHARMM in GROMACS is described, the authors say that: "Electrostatics was treated with particle-mesh Ewald (PME), using a short-range cutoff of 1.2 nm, and van der Waals intera

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

On 2/26/13 11:47 AM, francesco oteri wrote: Thank you Justin, I added rlistlong = 1.4 but still grompp complains: NOTE 1 [file 02md.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. Why doesn't grompp looks for rlistlong va

Re: [gmx-users] mdrun WARING and crash

On 2/26/13 11:57 AM, l@utwente.nl wrote: Dear all, I got WARNING after mdrun, which says: "WARNING: Listed nonbonded interaction between particles 794 and 797 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction insid

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

On 2/26/13 12:01 PM, francesco oteri wrote: I am using 4.5.5...Is it OK? If it's giving a note about that, then clearly not. Try 4.6. But as I said, there's nothing actually wrong. -Justin 2013/2/26 Justin Lemkul On 2/26/13 11:47 AM, francesco oteri wrote: Thank you

[gmx-users] Re: [gmx-developers] 【file tpx versio】how to convert the version

Please post usage questions to gmx-users, not gmx-developers. I will CC this reply to gmx-users and ask that the discussion continue there. On 2/26/13 12:05 PM, 何斌 wrote: Hi: everyone. I has got that the error: //

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2/26 francesco oteri Thank you so much for the help! 2013/2/26 Justin Lemkul On 2/26/13 12:01 PM, francesco oteri wrote: I am using 4.5.5...Is it OK? If it's giving a note about that, then clearly not. Try 4.6. But as I said, there's nothing actually wrong. -Justin 201

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