Re: [gmx-users] Average number of salt bridge

2013-11-18 Thread Justin Lemkul
On 11/14/13 10:18 PM, bharat gupta wrote: Hi, How can I calculate the average number of salt bridges between two residues during the entire simulation ??... Unless you've got some wildly noncanonical residues, this is a binary function. Either the salt bridge exists (1) or does not (0).

Re: [gmx-users] how to pull both side

2013-11-18 Thread Justin Lemkul
On 11/17/13 8:48 AM, Tom wrote: Dear All, Can gromacs pull both sides (end) of a body way? for example pulling two end of a cylinder unitl it breaks. I knew Gromacs can pull two bodies (A and B) objects away. Can someone inform about this functionality of pulling (both sides/end of a same

Re: [gmx-users] energy minimization erorr

2013-11-18 Thread Justin Lemkul
On 11/18/13 2:36 AM, Archana Sonawani-Jagtap wrote: Hi, I am simulating a peptide in TFE-water system. I am getting following error: 1 particles communicated to PME node 4 are more than 2/3 times the cut-off out o f the domain decomposition cell of their charge group in dimension x. This

Re: [gmx-users] RF0 and g_energy

2013-11-18 Thread Justin Lemkul
On 11/18/13 10:40 AM, Williams Ernesto Miranda Delgado wrote: Hello I made a rerun on a MD simulation using Reaction-Field-zero for electrostatics. When I analyze the *.edr file with g_energy, there appears Coul-SR and Coul-14. How can I get the Coulomb long range term? This is very important

Re: [gmx-users] installing latest version of gromacs 4.6.3

2013-11-18 Thread Justin Lemkul
On 11/18/13 11:54 AM, vansh wrote: do i need to source it every time i will use gromacs ?? as this is what happening in my case.. If you don't configure your shell startup scripts to do it for you, yes. Otherwise, the 'source' statement can be added to whatever startup script your shell

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 115, Issue 69

2013-11-18 Thread Justin Lemkul
On 11/18/13 5:05 PM, Hari Pandey wrote: Dear Dr. Tsjerk, Many many thanks for your help. This makes me some sense but still I am confused about that you indicated me to look out the gromacs/share directory. In my gromacs, I have following directory tree: gromacs/share/gromacs/top I did not

Re: [gmx-users] ZN ion not in force field database

2013-11-19 Thread Justin Lemkul
On 11/19/13 5:54 AM, Prashant wrote: Dear Users, i am new to MD SIMULATION field therefore excuse me for my beginner's queries .I wanted to run MD using CHARMM27 force field on my protein which has Zn ion as a co factor but while creating topology i encountered an error that Zn ion is not in

Re: [gmx-users] error in running pdb2gmx

2013-11-19 Thread Justin Lemkul
On 11/18/13 6:10 AM, hasthi wrote: Dear Justin, Thank you for your reply. Yeah I have modified my force field to include the phosphorylated Serine residue. Below is the pdb2gmx command employed pdb2gmx -f alpha_ser129p.pdb -o alpha_sep129p.gro -ff gromos43a1 -ignh error :

Re: [gmx-users] (no subject)

2013-11-19 Thread Justin Lemkul
On 11/19/13 11:31 AM, Mohsen Ramezanpour wrote: Hi I think you should use the correct atomtype, accoding to this FF atomtypes, for your atom which you have introduced as HH. Correct. More explicitly, the trick to dealing with OPLS-AA is that its nonbonded types (opls_*) have bonded

Re: [gmx-users] I can't re-image molecule for multiple MD without trjcat them from start

2013-11-19 Thread Justin Lemkul
On 11/19/13 11:13 AM, Asaminew Haile wrote: Hi Gromacs Users I'm new for gromacs analysis I'm running MD in a 40 ns time interval. I want to strip the water and re-image the molecule. But I found that only if I trjcat all trajectories from the start I can be able to re-image them. Can someone

Re: [gmx-users] QM guy at wits' end

2013-11-20 Thread Justin Lemkul
On Wed, Nov 20, 2013 at 2:07 PM, SAllen alle...@email.unc.edu wrote: Hello, I want to run MD simulations on a series of macrocycles that contain a lot of non-standard residues (dehydroalanines, dehydrobutyrines, 1,3-thiazoles, and a pyridine for good measure). I've been coming the internets

Re: [gmx-users] topology file for n-propanol

2013-11-20 Thread Justin Lemkul
On Wed, Nov 20, 2013 at 4:53 PM, Ehsan Sadeghi es...@sfu.ca wrote: Thanks Justin. Could you explain more? You meant that I don't need topology file for propanol? How about g_b, g_a, g_d values? You need a topology, but what I'm saying is that it is very easy to do. CH3 and CH2 groups are

Re: [gmx-users] GPU g_energy problem

2013-11-26 Thread Justin Lemkul
On Mon, Nov 25, 2013 at 3:40 AM, Andrei Neamtu neamtuand...@gmail.comwrote: Dear GMX users, I am simulating a system of two proteins in TIP4P water box. The simulations are performed on a system with 3 servers each containing 16 CPU cores and 2 Tesla 2090 GPU. The problem thai I encounter

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 115, Issue 117

2013-11-26 Thread Justin Lemkul
On Tue, Nov 26, 2013 at 8:08 AM, sunita gupta sunita@gmail.com wrote: Thanks Justin, Its strange that some atomtypes like ha, h1, n2 etc whose parameters are already present in the gbsa.itp are also not recognised. I have many more ligands to deal with. Can you tell me how to overcome

Re: [gmx-users] step 0Segmentation fault: 11

2013-11-26 Thread Justin Lemkul
On 11/26/13 6:31 PM, Valentina wrote: The problems I have eliminated: 1. Number of processors and threads - I am running on 1 2. Atomic overlap - none I have checked my bonded wells and my atomic distances are very similar. The init was originally minimised with DFT. 3. LINCS - I get same

Re: [gmx-users] gen_vel

2013-11-27 Thread Justin Lemkul
On 11/26/13 11:48 PM, Mahboobeh Eslami wrote: Hi Dear Gmx Users, Do not just following procedure can be usedby gen_vel: NVT gen_vel = yes gen_temp=300 gen_seed=-1 NPT gen_vel=no MDgen_vel=no i want to study the changing of velocity in md stage. Can I use the

Re: [gmx-users] calculate velocity autocorrelation function

2013-11-27 Thread Justin Lemkul
On 11/27/13 1:16 AM, Mahboobeh Eslami wrote: hi Dear Gmx Users please help me i want to calculate velocity autocorrelation function by gromacs but I do not know exactly what is needed. Please Help me, please g_velacc -h -Justin -- ==

Re: [gmx-users] step 0Segmentation fault: 11

2013-11-27 Thread Justin Lemkul
On 11/27/13 7:30 PM, Valentina wrote: I still cannot resolve this problem. Is there any way to find out what is causing Segmentation Fault? Normally Gromacs provides quite comprehendible errors, but this one. I have checked the charges against DFT. I also have the output of the system

Re: [gmx-users] free energy landscape

2013-11-28 Thread Justin Lemkul
On 11/28/13 7:20 AM, aixintiankong wrote: Dear, i want to make a free energy landscape with respect to Rg and RMSD. First i get the rmsd.xvg by g_rms and then get the Rg.xvg file by g_gyrate. And the i merge the rmsd value and Rg value into one file with two column, then i use the g_sham

Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Justin Lemkul
On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote: Maybe you should modify your .tpr file manually according to what you added in the previous sections! Manually modify a .tpr? How would one do that? The OP needs to provide the exact commands issued. The fatal error shown results from poor

Re: [gmx-users] For GMX implicit solvent MD

2013-11-28 Thread Justin Lemkul
On 11/28/13 9:31 AM, dxl...@hotmail.com wrote: Dear All, I'd like to do some implicit solvent MD with Gromacs. However, I meet a trouble. For instance, I have included gbsa.itp. when I used a SPC water molecule for Implicit Sovent MD,it goes very well. Then when I use two SPC water

Re: [gmx-users] AMBER99sb-ILDN force field and TIP4P water model

2013-11-28 Thread Justin Lemkul
On Thu, Nov 28, 2013 at 6:37 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Oh, I am sorry, I made a big mistake! :) Best Regards On Thu, Nov 28, 2013 at 6:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/28/13 9:37 AM, Mohsen Ramezanpour wrote: Maybe you should modify your

Re: [gmx-users] pdb2gmx fails because of imaginary Residue E

2013-11-29 Thread Justin Lemkul
On 11/29/13 7:23 PM, kolnkempff wrote: pdb2gmx produces error message: Fatal error: Residue 'E' not found in residue topology database But there is no Residue 'E' in my pdb file (see below). I have verified that all residues in the pdb file are listed in ffamber03.rtp and pdb2gmx does

Re: [gmx-users] Umbrella Sampling tutorial

2013-11-30 Thread Justin Lemkul
On 11/30/13 9:22 AM, shahab shariati wrote: Dear Justin My system contains lipid bilayer + drug + water molecules. I want to calculate Potential of mean force as a function of the distance between the centers of mass of drug and the lipid bilayer. Based on your suggestion I used

Re: [gmx-users] double precision and minimisation error

2013-11-30 Thread Justin Lemkul
On 11/30/13 9:29 AM, jkrie...@mrc-lmb.cam.ac.uk wrote: As has been asked a number of times before, I have seen minimization halt at a low number of steps having converged to machine precision when double precision is not used - does that not mean that double precision is needed at least for

Re: [gmx-users] simulated anealing

2013-12-01 Thread Justin Lemkul
On 12/1/13 2:48 AM, kiana moghaddam wrote: Dear GMX Users I want to run NVT equilibration and NPT equilibration (after NVT) for DNA-ligand interaction and want to increase temperature gradually i.e. from 0 to 300 K over a 100 ps, but i have some questions about this process: when I use

Re: [gmx-users] Umbrella Sampling tutorial

2013-12-01 Thread Justin Lemkul
On 12/1/13 8:04 AM, shahab shariati wrote: Dear Justin Very thanks for your reply I will slow pulling by changing pull_rate1 from 0.01 to 0.001 and pull_k1 from 1000 to 100. I have a basic question. Before minimization, where should I put drug molecule? into water molecules or into lipid

Re: [gmx-users] gen_seed

2013-12-01 Thread Justin Lemkul
On 12/1/13 9:45 AM, Mahboobeh Eslami wrote: Hi Dear Gmx Users what is the different between gen_seed= -1 and gen_seed=173529? From the manual: when gen-seed is set to -1, the seed is calculated from the process ID number. The other is just a default value that has no particular

Re: [gmx-users] Umbrella Sampling tutorial

2013-12-01 Thread Justin Lemkul
On 12/1/13 10:38 AM, shahab shariati wrote: Dear Justin When I placed drug within the lipid bilayer, after Generating Configurations step, I obtained 501 gro files. When I used distance.pl script for these gro files, my summary_distances.dat file is as follows: 00.2756352 10.2535359

Re: [gmx-users] Invalid order for directive implicit_genborn_params

2013-12-01 Thread Justin Lemkul
On 12/1/13 9:51 PM, rdwducl wrote: Hello, I am trying to use implicit solvation but I am getting the following error from the preprocessor: --- Program grompp_mpi, VERSION 4.6.4 Source code file:

Re: [gmx-users] Atomistic Simulation

2013-12-03 Thread Justin Lemkul
On 12/3/13 6:17 AM, Hardy, Adam wrote: I've just started doing atomistic simulations over the last few weeks as well and can share what I've learned so far. I have been using 'automated topology builder'. It only uses the gromos 53a6 forcefield so eliminates the choice if you want to use

Re: [gmx-users] heating

2013-12-03 Thread Justin Lemkul
On 12/3/13 2:17 AM, kiana moghaddam wrote: Dear GMX Users I want to run NVT equilibration and NPT equilibration (after NVT) and want to increase temperature gradually i.e. from 0 to 300 K over 100 ps, but I have some questions about this process: when I use simulated annealing in NVT as

Re: [gmx-users] g_msd -trestart

2013-12-03 Thread Justin Lemkul
On 12/3/13 10:02 AM, jwill...@andrew.cmu.edu wrote: Does anyone know exactly what g_msd -trestart does? I have a 60ns trajectory and used -trestart 1000 and the results said: Used 30 restart points spaced 1000 ps over 60001 ps Shouldn't it be 60 restart points? Maybe this will help:

Re: [gmx-users] Using several cores for MD production

2013-12-03 Thread Justin Lemkul
On 12/3/13 10:23 AM, MUSYOKA THOMMAS wrote: Dear Users, I am using a cluster of 64 cores to perform my MD simulations using GROMACS version 4.5.5. I would be glad to know the exact mdrun command that will allow me use the available resources. The answer depends entirely on the

Re: [gmx-users] constraint in Production

2013-12-04 Thread Justin Lemkul
On 12/3/13 11:43 AM, kiana moghaddam wrote: Dear Users I have a problem about production step in MD simulation. Can this step be run with constraints or unconstraints? Whether or not you use constraints depends on whether you need them. It is quite common to constrain at least the bonds

Re: [gmx-users] Bug #554: pdb2gmx proton naming compliancy

2013-12-04 Thread Justin Lemkul
On 12/3/13 4:51 PM, Kibalchenko, Mikhail wrote: Dear Users, does anyone know what was the resolution of this bug? http://redmine.gromacs.org/issues/554 How does one handle pdb2gmx with PDB files and avoid errors like this? Atom HB3 in residue ASP 2 was not found in rtp entry ASP with 14

Re: [gmx-users] out of disk space error

2013-12-04 Thread Justin Lemkul
On 12/4/13 5:24 AM, a...@imtech.res.in wrote: I think so. You are outputting the information too often i.e every 0.2 ps i.e. 5000 times per ns. See this thread http://comments.gmane.org/gmane.science.biology.gromacs.user/32721 It is unlikely that a few hundred ps of NVT would fill up

Re: [gmx-users] Fwd: Warning while loading .gro generated from .pdb with pdb2gmx

2013-12-04 Thread Justin Lemkul
On 12/4/13 5:33 AM, Pacho Ramos wrote: When I convert attached .pdb file to .gro using: pdb2gmx -quiet -ff amber99 -water none -f ${MOL}.pdb -o ${MOL}Initial.gro -i ${MOL}.itp -p ${MOL}.top -ignh the generated .gro file causes vmd (1.9.1) to show this warning while loading it: Warning)

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread Justin Lemkul
On 12/4/13 6:15 AM, panzu wrote: Hello users, After downloading the toluene.pdb file of a toluene molecule and its forcefield tolu.itp from Automated Topology Builder and saved in the root /usr/share/gromacs/top/gromos53a6.ff I use the next comand i order to convert the pdb format to .gro :

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread Justin Lemkul
On 12/4/13 9:06 AM, panzu wrote: so How do I convert from .pdb to .gro the ? You don't technically need one: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File If you prefer to use .gro format, just convert with editconf. The job of pdb2gmx is to produce a topology; the

Re: [gmx-users] Atomistic Simulation

2013-12-04 Thread Justin Lemkul
On 12/4/13 9:50 AM, panzu wrote: The thing is when I tray to use the grompp comand: bash g_grompp -f grompp.mdp -c tolu.pdb -p topol.top Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# NOTE 1 [file grompp.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting

Re: [gmx-users] force field for prodrg server

2013-12-04 Thread Justin Lemkul
On 12/4/13 10:24 AM, Mahboobeh Eslami wrote: hi dear Justin You've written the following context in your tutorial: Force field (GROMOS96.1/GROMOS87): GROMOS96.1 refers to the first version of the GROMOS96 force field, 43A1. GROMOS87 refers to the (outdated!) GROMOS87 force field. Choose

Re: [gmx-users] deformation in cnt

2013-12-04 Thread Justin Lemkul
On 12/4/13 10:48 AM, Atila Petrosian wrote: Dear Justin Thanks for your reply z dimension of box is exactly equal to the length of the cnt axis. The box size should be (length of CNT) + (bond length). What value is appropriate for bond length to add length of CNT? Whatever the lengths

Re: [gmx-users] force field for prodrg server

2013-12-04 Thread Justin Lemkul
always derive the parameters from scratch yourself ;) -Justin On Wednesday, December 4, 2013 7:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/4/13 10:24 AM, Mahboobeh Eslami wrote: hi dear Justin You've written the following context in your tutorial: Force field (GROMOS96.1

Re: [gmx-users] Fwd: Warning while loading .gro generated from .pdb with pdb2gmx

2013-12-04 Thread Justin Lemkul
and it rarely means anything. Your topology within Gromacs is definitive. External software is not. -Justin 2013/12/4 Justin Lemkul jalem...@vt.edu On 12/4/13 5:33 AM, Pacho Ramos wrote: When I convert attached .pdb file to .gro using: pdb2gmx -quiet -ff amber99 -water none -f ${MOL}.pdb

Re: [gmx-users] atom name - topology

2013-12-04 Thread Justin Lemkul
On 12/4/13 11:48 AM, Steven Neumann wrote: Dear Gmx Users, My molecule contains 2516 atoms made of 5 type of beads: BAS, POL, NON, ACI, GLY and I want to create a topology. Is it possible to make one residue of one [ moleculetype ] with this number of atoms so that: [ moleculetype ] ; Name

Re: [gmx-users] atom name - topology

2013-12-05 Thread Justin Lemkul
is define each residue as if it were a polymer, then you don't have to worry about 2500+ unique atom names. If each unit is only a few beads, this becomes trivial to do and pdb2gmx will do all the work via .rtp entry. -Justin Steven On Wed, Dec 4, 2013 at 5:37 PM, Justin Lemkul jalem...@vt.edu

Re: [gmx-users] segment fault when using editconf

2013-12-05 Thread Justin Lemkul
On 12/5/13 5:38 AM, sunyeping wrote: Dear gromcas users, I have a receptor-ligand complex pdb file, and I want to use editconf to generate the receptor pdb file and the ligand pdb file. I use the following commands:editconf -f _comp0.pdb -o _receptor0.pdb -n index.ndxeditconf -f _comp0.pdb -o

Re: [gmx-users] question

2013-12-05 Thread Justin Lemkul
On 12/5/13 6:10 AM, Andrew Bostick wrote: Hi gmx users I am beginner in gromacs. Excuse me for my simple and ordinary questions. --- 1) In the most of tutorials and papers I read to now, for the simulation of

Re: [gmx-users] exclusions

2013-12-05 Thread Justin Lemkul
On 12/5/13 9:48 AM, Steven Neumann wrote: Dear Gmx Users, How can I apply exclusions of non-bonded parameters within my [moleculetype] - I the positions of this molecule is restrained so all non-bonded should be excluded. Would that need [ exclusions ] or energy-monitor group can be applied?

Re: [gmx-users] exclusions

2013-12-05 Thread Justin Lemkul
On 12/5/13 10:28 AM, Steven Neumann wrote: I guess I need to write [ exclusions ] as TUB is composed of other energygrps. I have 2516 atoms, that would be difficult to write [ exclusions ] manually, would you recommend any script? I am not programming :( It's an easy loop. Every atom is

Re: [gmx-users] Fwd: How can i run my system successfully?

2013-12-07 Thread Justin Lemkul
On 12/7/13 4:51 AM, bahareh khanoom wrote: Dear friend thanks for your answer first i generate DRG.itp for adsorbed molecules, by PRODRG server. next i optimize adsorbed moleculs by gaussian b3lyp/6-311++g(d) opt Pop=ChelpG and the end ,i replaced the charges in DRG.itp with charges that

Re: [gmx-users] end capping

2013-12-07 Thread Justin Lemkul
On 12/7/13 8:11 AM, Shine A wrote: Sir, I am using MD to study the folding of peptides. Now I want to modify N terminal of the peptide with acetyl group and C terminus with amide group.How Can I do this? What are the changes I should made in various files? Gromos96 53a6 is using for

Re: [gmx-users] Fwd: How can i run my system successfully?

2013-12-08 Thread Justin Lemkul
thanks in advance bahar On Sat, Dec 7, 2013 at 4:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/7/13 4:51 AM, bahareh khanoom wrote: Dear friend thanks for your answer first i generate DRG.itp for adsorbed molecules, by PRODRG server. next i optimize adsorbed moleculs by gaussian b3lyp/6

Re: [gmx-users] simulation using tabulated dihedral potentials.

2013-12-09 Thread Justin Lemkul
On 12/9/13 8:09 AM, Chandan Choudhury wrote: On Mon, Dec 9, 2013 at 5:41 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Do your tabulated functions work on a toy system, like butane? No Mark. I didnot try with butane. The simulation stops when I incorporated tabulated dihedral potential.

Re: [gmx-users] what is the mean sar, st, pi, gar and hct of gbsa.itp?

2013-12-10 Thread Justin Lemkul
On Tue, Dec 10, 2013 at 8:11 AM, C.H. Kim poc...@icloud.com wrote: Dear All. Hi. I'm want calculation of dimer protein. My proteins have manganese. But don't have gbsa.itp of manganese. I'm insert Mn data, but I don't know 'sar, st, pi ...' What is the values mean? Please read manual

Re: [gmx-users] ligand covalently bond with the protein

2013-12-10 Thread Justin Lemkul
On Tue, Dec 10, 2013 at 7:54 AM, aixintiankong aixintiank...@126.comwrote: Dear , I want to bulid a system that the ligand covalently bond with the protein, could anyone tell how to do this one by one step or give me a tutorial to do this. thank you very much !

Re: [gmx-users] why it is symmetric

2013-12-10 Thread Justin Lemkul
On Mon, Dec 9, 2013 at 12:58 PM, Albert mailmd2...@gmail.com wrote: Hello: I am calculating the water density inside my membrane protein along Z directions. I used the a_ri3DC tool in Gridcount which is a patch in Gromacs for calculation: a_ri3Dc -grid gridxdr.dat -profile profile.xvg -xyp

Re: [gmx-users] OPLS force field issue

2013-12-10 Thread Justin Lemkul
On Mon, Dec 9, 2013 at 3:05 PM, Ehsan Sadeghi es...@sfu.ca wrote: Thanks Justin. I added the bond description in the ffbonded.itp but it does not show in the topol.top file. In ffbonded.itp we have: [ bondtypes ] ; ij func b0 kb OWHW 10.09572

Re: [gmx-users] deformation in cnt

2013-12-10 Thread Justin Lemkul
On Tue, Dec 10, 2013 at 4:02 AM, Atila Petrosian atila.petros...@gmail.comwrote: Dear Justin Based on your suggestion, I added C-C bond length to z dimension of box (before: 5.5 3.5 3.5, now: 5.5 3.5 3.6418). Then I used genion to neutralize system using replacing 2 water molecules by 2

Re: [gmx-users] Strange trjconv error

2013-12-10 Thread Justin Lemkul
On Tue, Dec 10, 2013 at 8:55 AM, rajat desikan rajatdesi...@gmail.comwrote: Hi All, I have a NPT NAMD trajectory of a membrane-protein that I want to analyze in gromacs 4.6.3. (g_density). I used catdcd to convert the .dcd to .pdb and generated a .top from the .psf using topotools in vmd. I

Re: [gmx-users] constraining protein in the box

2013-12-10 Thread Justin Lemkul
On Tue, Dec 10, 2013 at 12:31 PM, Shine A shin...@iisertvm.ac.in wrote: Sir, I completed a 400 ns MD simulation. But in some part of the trajectory my protein is just out side the box I selected (triclinic). Is there any option in gromacs to constrain my protein in box during simulation.

Re: [gmx-users] ligand covalently bond with the protein

2013-12-10 Thread Justin Lemkul
On Tue, Dec 10, 2013 at 7:28 PM, aixintiankong aixintiank...@126.comwrote: Dear , I want to bulid a system that the ligand covalently bond with the protein, could anyone tell how to do this one by one step or give me a tutorial to do this. thank you very much ! Please refer to the link

Re: [gmx-users] Strange trjconv error

2013-12-11 Thread Justin Lemkul
10, 2013 at 8:28 PM, Justin Lemkul jalem...@vt.edu wrote: On Tue, Dec 10, 2013 at 8:55 AM, rajat desikan rajatdesi...@gmail.com wrote: Hi All, I have a NPT NAMD trajectory of a membrane-protein that I want to analyze in gromacs 4.6.3. (g_density). I used catdcd to convert the .dcd

Re: [gmx-users] deformation in cnt

2013-12-11 Thread Justin Lemkul
On Wed, Dec 11, 2013 at 3:39 AM, Atila Petrosian atila.petros...@gmail.comwrote: Dear Justin Thanks for your reply. After energy minimization, all carbon atoms are in true position, inside box but again, both ends of cnt were deformed, same problem I had before I add bond length to the

Re: [gmx-users] deformation in cnt

2013-12-11 Thread Justin Lemkul
On Wed, Dec 11, 2013 at 10:05 AM, Atila Petrosian atila.petros...@gmail.com wrote: Dear Justin I built CNT by nano tube modeller. Then, I put protein (fragment model with 15 residues) in appropriate distance of CNT manually. I used force field parameters from following paper: J. Phys.

Re: [gmx-users] OPLS force field parameters

2013-12-12 Thread Justin Lemkul
On Thu, Dec 12, 2013 at 12:45 PM, Ehsan Sadeghi es...@sfu.ca wrote: Hi gmx users, I try to use OPLS force field for my simulation. I added the following residue to the aminoacids.rtp, but when I generate the topol.top file it does not show the the bond stretching, angle bond, dihedrals. [

Re: [gmx-users] OPLS force field parameters

2013-12-13 Thread Justin Lemkul
to those numbers, and fix ffbonded.itp as needed. -Justin Kind regards, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-us...@gromacs.org Sent: Thursday, December 12, 2013 3:02:22 PM Subject: Re: [gmx-users] OPLS force field

Re: [gmx-users] Installing Gromacs 4.6.3 using Cygwin

2013-12-13 Thread Justin Lemkul
On Fri, Dec 13, 2013 at 3:38 PM, chem grad kelly.summ...@usask.ca wrote: Actually... yes, I may have spoken too soon... I can see Gromacs on my machine, but I am still struggling to get it to run properly. I cannot convince cygwin to source the gromacs files properly (well, at least I think

Re: [gmx-users] missing residues in pdb file

2013-12-14 Thread Justin Lemkul
On Sat, Dec 14, 2013 at 7:03 AM, delara aghaie d_agh...@yahoo.com wrote: Dear Gromacs users, I am going to simulate human serum albumin( HSA) .. The pdb file contains warfarin as well. Now I have two questions: 1) to delete warfarin which lines should be removed? only those starting with

Re: [gmx-users] question_gromacs

2013-12-15 Thread Justin Lemkul
On Sun, Dec 15, 2013 at 3:20 AM, Andrew Bostick andrew.bosti...@gmail.comwrote: Dear Gromacs users I have following error when I do equilibration: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 0.8875 nm Change the number of

Re: [gmx-users] How to find the mutation effect?

2013-12-15 Thread Justin Lemkul
On Sun, Dec 15, 2013 at 1:42 PM, xiao helitr...@126.com wrote: Dear all, I am doing a MD on a mutant protein which is unstable from exprient. However, i found no difference between the wild type and the mutant protein from md, the structure and the rmsd are very similar in the mutant and the

Re: [gmx-users] fractional charge

2013-12-16 Thread Justin Lemkul
On Mon, Dec 16, 2013 at 2:42 AM, ansu...@physics.iisc.ernet.in wrote: Dear gromacs users, I have run pdb2gmx for dimer with one MG ion in each chain. 1) If I run without Mg the total charge is -8.00 (-4.00 in each chain) 2) If I run with Mg the total charge becomes : a) -4.00 for A chain

Re: [gmx-users] OPLS force field issue....

2013-12-16 Thread Justin Lemkul
On Mon, Dec 16, 2013 at 4:06 PM, Sidath Wijesinghe swij...@g.clemson.eduwrote: Dear Friends, i have done a MD simulation using OPLS/AA in lammps which contains 7930 atoms. i want to run this in Gromacs so i followed this step g_x2top -f test.pdb -o np1.top -name np1 -ff oplsaa -pbc (

Re: [gmx-users] Gromos DPPC bilayer: different results for 4.0.7 and 4.6.5

2013-12-16 Thread Justin Lemkul
On Mon, Dec 16, 2013 at 3:10 PM, Lutz Maibaum lutz.maib...@gmail.comwrote: I am running MD simulations of DPPC bilayers with the Gromos force field, and I am seeing some differences between using Gromacs 4.0.7 and 4.5.5/4.6.5 that I do not understand. It would be great if someone had any

Re: [gmx-users] Pressure coupling in NPT equilibration step

2013-12-16 Thread Justin Lemkul
On Mon, Dec 16, 2013 at 2:42 PM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi GMX user please help me i want to study protein ligand complex by gromacs4.6.3. i repaired my protein by MODELER and docked my ligand by AUTODOCK software. i use amber99sb-ildn force field. after

Re: [gmx-users] OPLS force field issue....

2013-12-16 Thread Justin Lemkul
On Mon, Dec 16, 2013 at 8:09 PM, Sidath Wijesinghe swij...@g.clemson.eduwrote: Justin, Thank you for the reply. so that means i need to place the parameters in atomname2type.n2t file? Yes, per the format shown on that site. I will warn you that it can be difficult to define non-overlapping

Re: [gmx-users] Berendsen and Parrinello-Rahman

2013-12-16 Thread Justin Lemkul
On Mon, Dec 16, 2013 at 3:19 AM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi all my friends i am studying protein-ligand complex by gromacs 4.6.3 i see followingText in gromacs site: Berendsen is often the best algorithm for equilibration, because it is the most robust to the

Re: [gmx-users] OPLS force field issue....

2013-12-17 Thread Justin Lemkul
On Tue, Dec 17, 2013 at 10:09 AM, Sidath Wijesinghe swij...@g.clemson.eduwrote: Justin, so that means delete these lines ATOM 7882 SOD UNK 1 42.69 -261.86 64.056 1.00 0.00 UNK ATOM 7883 SOD UNK 1 39.09 -260.89 62.8968 1.00 0.00 UNK ATOM 7884 SOD

Re: [gmx-users] selection around circle

2013-12-17 Thread Justin Lemkul
On 12/17/13 1:55 PM, jkrie...@mrc-lmb.cam.ac.uk wrote: I think g_select does something like this. I am trying to do something similar: make a selection of water within 5A or so of a residue in my protein. Also need help please. The examples at the end of g_select -select 'help all' pretty

Re: [gmx-users] About free energy Methods for Memebrane-protein Calculation

2013-12-18 Thread Justin Lemkul
On 12/18/13 9:57 AM, vidhya sankar wrote: Dear Justin , Thank you for your Previous reply. I am Doing Simulation of assembly of Cyclic Petide in POPC membrane For that I need to calculate Free energy for Stability of Assembly. Normally Membrane Tutorail Does not

Re: [gmx-users] g_tcaf issue

2013-12-18 Thread Justin Lemkul
On 12/18/13 1:21 PM, Jones de Andrade wrote: Hi Justin. Thanks for the suggestion. Unfortunately, only today we could work on the problem again. We recompiled it with option -DCMAKE_BUILD_TYPE=DEBUG on the cmake step. After, we ran the gdb g_tcaf to get the following: gdb g_tcaf_mpi GNU

Re: [gmx-users] table-extension distance appears to be over-ridden by .mdp file cut-off values

2013-12-18 Thread Justin Lemkul
Caveat to start: I am not an expert on tabulated potentials, but I'll take a crack at helping in case it inspires a solution :) Very thorough report, so thanks for providing an exemplary level of detail. On 12/18/13 3:39 PM, Elizabeth Ploetz wrote: Dear Gromacs Users, I'm trying to use

Re: [gmx-users] OPLS force field issue....

2013-12-18 Thread Justin Lemkul
well for complex systems. if i find the parameters for the missing parameters how can i get rid of sodium as u mentioned for the real system with Na+ ions? I answered this question in my previous message. -Justin Thank you! On Wed, Dec 18, 2013 at 9:37 PM, Justin Lemkul jalem...@vt.edu

Re: [gmx-users] RMSD per residue

2013-12-19 Thread Justin Lemkul
On 12/19/13 6:03 AM, Saman Shahriyari wrote: Dear users I am trying to have the RMSD per residue profile of my trajectory. i approached this by using g_rmsf tool with -od and -res options. although i can have such profile, but it seems that the average structure of my trajectory is being

Re: [gmx-users] OpenMM Compatibility issues with GPU build

2013-12-19 Thread Justin Lemkul
On 12/19/13 2:02 AM, Seera Suryanarayana wrote: Dear Gromacs users, I have successfully installed a) cudatoolkit_4.2.9_linux_64_ubuntu11.04.run b) devdriver_4.2_linux_64_295.41.run c) gpucomputingsdk_4.2.9_linux.run d) OpenMM 4.1 from Source e) GROMACS 4.6.5 While trying to install / cmake

Re: [gmx-users] OPLS force field issue....

2013-12-19 Thread Justin Lemkul
, Dec 18, 2013 at 9:50 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/18/13 9:46 PM, Sidath Wijesinghe wrote: Is g_x2top the only way for my situation? or am i in the wrong track? There are numerous ways to generate topologies. I have warned you that g_x2top is probably ill-suited

Re: [gmx-users] Implicit solvation: nonpolar term?

2013-12-19 Thread Justin Lemkul
On 12/19/13 5:47 PM, rdwducl wrote: Hello, I am using GBSA/OBC implicit solvation with an ACE-type approximation for the nonpolar term. Having looked at the GROMACS code, it would appear to be using the following form for the nonpolar free energy: sum_i 4*pi*tension*(R_i + R_s)^2 *

Re: [gmx-users] Implicit solvation: nonpolar term?

2013-12-19 Thread Justin Lemkul
On 12/19/13 6:14 PM, rdwducl wrote: Thanks for the reply Justin but I'm confused. Why must the atoms be bonded? Ultimately I plan to model micellisation whereby surfactants, which only interact with each other via non-bonded terms, are driven to aggregate by this nonpolar term... I'm

Re: [gmx-users] Implicit solvation: nonpolar term?

2013-12-20 Thread Justin Lemkul
On 12/19/13 7:33 PM, Robert Darkins wrote: On 19/12/13 23:31, Justin Lemkul wrote: On 12/19/13 6:14 PM, rdwducl wrote: Thanks for the reply Justin but I'm confused. Why must the atoms be bonded? Ultimately I plan to model micellisation whereby surfactants, which only interact with each

Re: [gmx-users] table-extension distance appears to be over-ridden by .mdp file cut-off values

2013-12-20 Thread Justin Lemkul
will be used for all other energy group pairs. From: Justin Lemkul [via GROMACS] ml-node+s5086n5013404...@n6.nabble.com Sent: Wednesday, December 18, 2013 20:23 To: Elizabeth Ploetz Subject: Re: table-extension distance appears to be over-ridden by .mdp file cut

Re: [gmx-users] GridMAT-MD gnuplot

2013-12-24 Thread Justin Lemkul
On 12/24/13, 9:59 AM, shahab shariati wrote: Dear gromacs users I used GridMAT-MD to obtain area per lipid and bilayer thickness. I used vector for output_format in param_example file. Based on the user guide for GridMAT-MD, when I used gnuplot: perl convert_to_gnuplot.pl

Re: [gmx-users] Calculating the displacement of an atom QUERY

2013-12-24 Thread Justin Lemkul
On 12/24/13, 2:38 AM, rbbioinfo wrote: Hi, I want to plot the total displacement of an atom/ion along Z axis with respect to time. Anybody kindly help me regarding how to calculate the movement of any atom using gromacs. An early response will be highly appreciated. Sounds like a job for

Re: [gmx-users] Potential energy calculations

2013-12-26 Thread Justin Lemkul
On 12/26/13, 5:30 AM, lloyd riggs wrote: Zero it-- If you plot a potential energy value strait from the simulation it will be something like point a) -7000 point b) -7050 across a single simulation. Thus you have to find a beginning point and subtract it across the run. Additionally,

Re: [gmx-users] question regarding free energy calculations

2013-12-26 Thread Justin Lemkul
On 12/25/13, 4:55 AM, Asaf Farhi wrote: Dear all Hi. We have a question regarding the implementation of free energy calculations in Gromacs that we have been trying for long time to decipher. The question is the following: When transforming molecule A to B if the non bonded interactions

Re: [gmx-users] Potential energy calculations

2013-12-27 Thread Justin Lemkul
:* Justin Lemkul jalem...@vt.edu *An:* gmx-us...@gromacs.org *Betreff:* Re: [gmx-users] Potential energy calculations On 12/26/13, 5:30 AM, lloyd riggs wrote: Zero it-- If you plot a potential energy value strait from the simulation it will be something like point a) -7000 point b) -7050 across

Re: [gmx-users] Potential energy

2013-12-27 Thread Justin Lemkul
On 12/27/13, 6:00 PM, Ali Alizadeh wrote: Dear All users, I have a question about calculation of potential energy for an especial group. I know I had to define an energy group in .mdp file. I forgot to do it. I want to know can I extract this potential energy by post processing or not? If

Re: [gmx-users] g_dist

2013-12-29 Thread Justin Lemkul
On 12/29/13, 8:17 AM, Andrew Bostick wrote: Dear gromacs users I know g_dist tool calculates the distance between the centers of mass of two groups of atoms as a function of time. How to obtain average distances of the selected atoms form the bilayer midplane. In this case, one group is

Re: [gmx-users] radial distribution function of fullerene COM and O of water

2013-12-29 Thread Justin Lemkul
On 12/29/13, 10:15 AM, mali wrote: Hi friends Have performed simulation of fullerene and water molecules and calculated free energy of solvation. Now want to calculate the radial distribution function of fullerene COM and O of water molecules. Could you please help how to perform it. Start

Re: [gmx-users] GROMACS zip file?

2013-12-29 Thread Justin Lemkul
On 12/29/13, 8:31 PM, Christian Wagner wrote: Dear All, I like to install GROMACS on a Windows 7 system. As indicated in the instructions section, I tried to download the GROMACS zip version for Windows from ftp://ftp.gromacs.org/pub/gromacs but I cannot connect to the site. On the

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