[gmx-users] gromacs-4.5.5 cpmd QM/MM versions

Dear All, I am planning to perform a QM/MM calculation of my protein system. Can anybody suggest me whether gromacs-4.5.5 can be patched with any latest version of CPMD? If not, then please suggest me some combination of the gromacs-cpmd versions. I came across this tutorial, but there, both groma

[gmx-users] gromacs-4.5.5 CPMD QM/MM

Dear All, I am planning to perform a QM/MM calculation of my protein system. Can anybody suggest me whether gromacs-4.5.5 can be patched with any latest version of CPMD? If not, then please suggest me some combination of the gromacs-cpmd versions. I came across this tutorial, but there, both groma

Re: [gmx-users] Potential Energy Scan

k On Thu, Aug 1, 2013 at 5:07 PM, Mark Abraham wrote: > http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy > > On Thu, Aug 1, 2013 at 7:03 AM, tarak karmakar > wrote: > > Dear All, > > > > Can anyone guide me how to perform the 'potential energy sc

[gmx-users] Potential Energy Scan

Dear All, Can anyone guide me how to perform the 'potential energy scan' for a dihedral of a small molecule in gromacs? Regrads, Tarak -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Sup

Re: [gmx-users] Protein RMSD high

raham wrote: > Your call. Is that motion significant to what you are trying to report > by your observation of the RMSD? > > Mark > > On Thu, Jun 27, 2013 at 9:03 AM, tarak karmakar > wrote: > > Dear All, > > > > While simulating a protein, I see the rmsd

[gmx-users] Protein RMSD high

Dear All, While simulating a protein, I see the rmsd fluctuates around a mean of 0.6 nm. I carefully looked at the trajectory (VMD movie) and saw there are two flexible terminii fluctuating with a very high amplitude contributing to the high value of RMSD. Is it ok to report this problem with this

Re: [gmx-users] High Initial generated Temp

> > On 6/4/13 12:51 PM, tarak karmakar wrote: > >> Yeah! >> It is indeed a silly point to generate a velocity distribution at 0 K. ( >> Maxwell-Boltzmann will be in trouble) >> After the warm up, now let say my protein is in 300 K, can't I generate a >>

Re: [gmx-users] High Initial generated Temp

73529 ) during my production run? Thanks, Tarak On Tue, Jun 4, 2013 at 10:10 PM, Justin Lemkul wrote: > > > On 6/4/13 12:17 PM, tarak karmakar wrote: > >> Thanks Justin. >> Sorry for not uploading the full .mdp. Here it is, >> >> ; 7.3.3 Run Control

Re: [gmx-users] High Initial generated Temp

I'm extremely sorry for copying the other '.mdp' file here. This is the modified one I just created after seeing your reply. In the previous case I didn't use 'continuation'. On Tue, Jun 4, 2013 at 9:47 PM, tarak karmakar wrote: > Thanks Justin. > Sorry for

Re: [gmx-users] High Initial generated Temp

ngs of how ligand is interacting with certain residues. So, then should I use these different velocity generating seeds during the warm up step? Thanks, Tarak On Tue, Jun 4, 2013 at 5:46 PM, Justin Lemkul wrote: > > > On 6/4/13 8:07 AM, tarak karmakar wrote: > >> Dear All, &g

[gmx-users] High Initial generated Temp

Dear All, Although I have set gen_temp = 300, it is showing the initial temperature 445.7 K, generated at the very beginning of the run. gen_vel = yes ; velocity generation gen_temp= 300 gen_seed= 93873959697 Is it because of a bad geo

[gmx-users] Re: OPLS-AA to CHARMM conversion in gromacs ffnonbonded.itp

All these parameters are for Mg2+, forgot to mention. On Fri, May 31, 2013 at 10:48 PM, tarak karmakar wrote: > Dear All, > > I have a little confusion with the non-bonding parameters conversion from > OPLS-AA to CHARMM in gromacs. > If I see the ffnonbonded.itp in both the

[gmx-users] OPLS-AA to CHARMM conversion in gromacs ffnonbonded.itp

Dear All, I have a little confusion with the non-bonding parameters conversion from OPLS-AA to CHARMM in gromacs. If I see the ffnonbonded.itp in both the cases I get the following numbers OPLS-GROMACS Sigma = 0.1644471 nm Epsilon = (0.875044*4.184) = 3.66118 kJ/mol

[gmx-users] charmm in gromacs cut-offs

Dear All, It seems the problem in the cut-off schemes while using charmm force field in gromacs persists even in the latest gromacs-4.6.1 version. Recently I have posted regarding this problem came in gromacs-4.5.5 version. If anybody has already tested this issue in the latest version, please

Re: [gmx-users] Inconsistent results in different clusters and cores

his mail went to you twice. Facing lot of problems, here, in mail delivery failure. Thanks, Tarak On Fri, May 17, 2013 at 6:22 PM, tarak karmakar wrote: > @ Justin and Mark, > > Do you have any idea about the rlist used by Bjelkmar et. al. > 'Implementation of charmm in gromacs

Re: [gmx-users] Inconsistent results in different clusters and cores

y 17, 2013 at 5:42 PM, tarak karmakar wrote: > I am extremely sorry for spaming the mail box. It was quite > unintentionally. Believe me I was getting the following error every > time while sending the mail. > > Final-Recipient: rfc822; jaanus.k...@eesti.ee > Action: failed >

Re: [gmx-users] Inconsistent results in different clusters and cores

...@eesti.ee Tarak -- Forwarded message -- From: tarak karmakar To: Discussion list for GROMACS users Cc: Date: Fri, 17 May 2013 15:50:25 +0530 Subject: Re: [gmx-users] Inconsistent results in different clusters and cores On Fri, May 17, 2013 at 5:36 PM, Mark Abraham wrote: >

Re: [gmx-users] Inconsistent results in different clusters and cores

I have read the 'implementation of charmm in gromacs' by bjelkmar, JCTC. There they have used following cut-offs coulombtype=PME rcoulomb=1.2 vdwtype=switch rvdw=1.2 rvdw-switch=1.0 I am not sure about rlist. Regards, Tarak On Fri, May 17, 2013 at 1:46 PM, tarak karmakar wrote:

[gmx-users] cut-offs

Dear All, I have read the 'implementation of charmm in gromacs' by bjelkmar, JCTC. There they have used following cut-offs coulombtype=PME rcoulomb=1.2 vdwtype=switch rvdw=1.2 rvdw-switch=1.0 If I use the same numbers with rlist=1.2 it is showing warning saying rlist should be at lear 0.1 - 0.3 n

[gmx-users] charmm in gromacs cut-offs

Dear All, I'm using charmm force field for simulation of a protein ligand system. I have read the paper "implementation of charmm in gromacs by Bjelkmar, JCTC' They have used the following set up coulombtype = PME rcoulomb= 1.2 vdwtype = switch rvdw

[gmx-users] charmm in gromacs cut-offs

Dear All, I'm using charmm force field for simulation of a protein ligand system. I have read the paper "implementation of charmm in gromacs by Bjelkmar, JCTC' They have used the following set up coulombtype = PME rcoulomb= 1.2 vdwtype = switch rvdw

[gmx-users] charmm in gromacs cut-offs

Dear All, I'm using charmm force field for simulation of a protein ligand system. I have read the paper "implementation of charmm in gromacs by Bjelkmar, JCTC' They have used the following set up coulombtype = PME rcoulomb= 1.2 vdwtype = switch rvdw

[gmx-users] charmm in gromacs cut-offs

Dear All, I'm using charmm force field for simulation of a protein ligand system. I have read the paper "implementation of charmm in gromacs by Bjelkmar, JCTC' They have used the following set up coulombtype = PME rcoulomb= 1.2 vdwtype = switch rvdw

[gmx-users] charmm in gromacs cut-offs

Dear All, I'm using charmm force field for simulation of a protein ligand system. I have read the paper "implementation of charmm in gromacs by Bjelkmar, JCTC' They have used the following set up coulombtype = PME rcoulomb= 1.2 vdwtype = switch rvdw

[gmx-users] charmm in gromacs cut-offs

Dear All, I'm using charmm force field for simulation of a protein ligand system. I have read the paper "implementation of charmm in gromacs by Bjelkmar, JCTC' They have used the following set up coulombtype = PME rcoulomb= 1.2 vdwtype = switch rvdw

Re: [gmx-users] Inconsistent results in different clusters and cores

hanks, Tarak On Fri, May 17, 2013 at 1:34 PM, tarak karmakar wrote: > What about Dispersion Correction ? > But if I use this set of informations > > ; 7.3.3 Run Control > integrator = md; md integrator > tinit = 0

Re: [gmx-users] Inconsistent results in different clusters and cores

n Sun, May 12, 2013 at 11:57 PM, tarak karmakar wrote: > Oh ! > Thanks a lot Justin. I'll rerun all my jobs with this corrected mdp. > Restrains things I didn't follow properly, anyway I'll read about this. > > > On Sun, May 12, 2013 at 11:27 PM, Justin Lemku

[gmx-users] 1-4 scaling factor

Dear All, How do I incorporate the 1-4 scaling factor ( e.g., 1.0 for CHARMM and 0.833 in AMBER) in gromacs? Or, is it internally taken care of by gromacs while specifying the -ff flag? NAMD input file uses the following keyword 1-4scaling 1.0 (for charmm force field) Thanks, Tara

Re: [gmx-users] Fwd: electrostatic potential map

xas at Austin > Department of Chemistry and Biochemistry > The Webb Group > > > On Mon, May 13, 2013 at 7:04 AM, tarak karmakar >wrote: > > > Dear All, > > > > I am running a simulation of ligand binding in a protein. Ligand is > > mostly negative

[gmx-users] Fwd: electrostatic potential map

Dear All, I am running a simulation of ligand binding in a protein. Ligand is mostly negatively charged, so as expected it should bind to the positive region of the protein. To check the possible binding zone, I try to calculate or rather visualize the electrostatic potential map of a protein

Re: [gmx-users] Inconsistent results in different clusters and cores

Oh ! Thanks a lot Justin. I'll rerun all my jobs with this corrected mdp. Restrains things I didn't follow properly, anyway I'll read about this. On Sun, May 12, 2013 at 11:27 PM, Justin Lemkul wrote: > > > On 5/12/13 1:53 PM, tarak karmakar wrote: > >> Thank

Re: [gmx-users] Inconsistent results in different clusters and cores

lincs_warnangle = 30 On Sun, May 12, 2013 at 11:11 PM, Justin Lemkul wrote: > > > On 5/12/13 1:34 PM, tarak karmakar wrote: > >> Thanks Justin for the Quick and Helpful reply. >> >> Yes. If I am right, the chaotic behavior of the simulations is >

Re: [gmx-users] Problem importing PDB to Gromacs

Remove all the hydrogens from the pdb file and then try to run pdb2gmx, I hope it'll do fine. Or you can also use -ignh option as suggested by Justin. Tarak On Fri, May 10, 2013 at 3:35 PM, Justin Lemkul wrote: > > > On 5/10/13 5:16 AM, Jernej Zidar wrote: > >> Hi, >>In CHARMM I generated

Re: [gmx-users] Inconsistent results in different clusters and cores

rote: > > > On 5/12/13 1:17 PM, tarak karmakar wrote: > >> Dear All, >> >> I am simulating a protein in water to check the ligand movement >> over a >> time span. I haveminimized the system in STEEP and CG and after that >> heated from

[gmx-users] Inconsistent results in different clusters and cores

Dear All, I am simulating a protein in water to check the ligand movement over a time span. I haveminimized the system in STEEP and CG and after that heated from 0K - 300K within a time span of 300 ps. Then, I performed the NPT production runs. In two clusters I have got different results

Re: [gmx-users] plots in gromacs

g/Support/Mailing_Lists > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe

Re: [gmx-users] how to build the loop of protein model

info/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.grom

[gmx-users] lysine side chain shrinking

Dear All, During a simulation of a protein with a ligand, I see the -NH3 of the lysine side chain near the ligand is getting squeezed for a very short time; N-H bonds are getting contracted and the angle are no longer within tetrahedral normal http://lists.gromacs.org/pipermail/gmx-users/2010-Nov

Re: [gmx-users] Re: Langevin Dynamics

Thanks Dr. Vitaly Yeap ! >From that point of view I'm seeing the correct temperature drift and it reaches nicely to 300 K after say, 300ps. But is it a good integrator ( SD ) to perform this job ? Or, should I opt for other, like Lep-frog or MD-VV with let say , Berendsen thermostat? Please expla

Re: [gmx-users] metal_ligand complex

Thanks Justin Yah! We can run steered MD or Umbrella Pulling ( sampling) for this purpose. But one thing I am wondering that how to move the entire complex. In my model there are no covalent bond ( bonding info) between the metal and ligands. So how to select a particular point in the complex to t

[gmx-users] COLVAR not printing

Dear All, I have copied and patched the plumed script plumed_gromacs-4.5.5.sh, given in the patches directory. But after doing that, while running some umbrella sampling it's not printing the COLVAR file, only the simple md is running there. So, can anyone help me in this regard? Thanks -- Tarak

Re: [gmx-users] Vizualization with VMD: no image appears

vmd protein.trr protein.gro then go to the representation and then write 'all not water' with cartoon representation, u will get the protein only. Cheers, Tarak On Thu, Nov 22, 2012 at 12:58 PM, rama david wrote: > Dear, >-o MT.PnoH.xtc instad of xtc extenstion use pdb you will get pdb file

Re: [gmx-users] Question about conserved energy in MTTK

Hi, I was also facing the same problem. If you check your pressure during this NPT run, u can see that it got increased to a higher value. I had posted the same problem few days back, u can follow the thread. It seems MTTK is not stable enough and is not performing well in this context. So I have

Re: [gmx-users] pressure_coupling

> Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- >> boun...@gromacs.org] Im Auftrag von tarak karmakar >> Gesendet: Mittwoch, 21. November 2012 15:03 >> An: Discussion list for GROMACS users >> Betreff: Re: [gmx-users] pressure_coupling >> >> Thanks for

Re: [gmx-users] pressure_coupling

tag, 20. November 2012 18:33 >> An: Discussion list for GROMACS users >> Betreff: Re: [gmx-users] pressure_coupling >> >> >> >> On 11/20/12 12:29 PM, tarak karmakar wrote: >> > Thanks Justin for the quick reply. >> > Is there any problem with the algor

Re: [gmx-users] pressure_coupling

parameters ? On Tue, Nov 20, 2012 at 10:10 PM, Justin Lemkul wrote: > > > On 11/20/12 11:26 AM, tarak karmakar wrote: >> >> Dear All, >> >> I want to keep the pressure at 1.0 bar during the NPT simulation. But >> it is fluctuating around 130 bar. So can an

Re: [gmx-users] constraining multiple types of bonds

thanks a lot Justin I'll try to follow this protocol. On Sun, Nov 11, 2012 at 8:59 AM, Justin Lemkul wrote: > > > On 11/10/12 10:27 PM, tarak karmakar wrote: >> >> Thanks Justin >> >> If I want to constrain all the bonds in the substrate molecule present

Re: [gmx-users] constraining multiple types of bonds

Thanks Justin If I want to constrain all the bonds in the substrate molecule present inside the enzyme cavity then along with SHAKE what I need to use ? On Fri, Nov 9, 2012 at 5:47 PM, Justin Lemkul wrote: > > > On 11/8/12 11:36 PM, tarak karmakar wrote: >> >> Thanks Ju

Re: [gmx-users] constraining multiple types of bonds

: Double entries in block structure. Item 5247 is in blocks 1371 and 1370 Cannot make an unambiguous inverse block. Please suggest me the exact protocol. Thanks On Fri, Nov 9, 2012 at 2:18 AM, Justin Lemkul wrote: > > > On 11/8/12 1:07 PM, tarak karmakar wrote: >> >> Dea

Re: [gmx-users] Double entries in block structure--problem with SHAKE

I'm bit confused how to implement constraints algorithm for these type of problem. Thanks On Wed, Nov 7, 2012 at 11:54 PM, Justin Lemkul wrote: > > > On 11/7/12 10:46 AM, tarak karmakar wrote: >> >> Dear All, >> >> As I am facing the following problem while

[gmx-users] Double entries in block structure--problem with SHAKE

Dear All, As I am facing the following problem while using SHAKE to constrain some bonds, I have checked the mailing list but I think, this issue has not been resolved. So if anyone knows the solution kindly inform me. Program mdrun, VERSION 4.5.5 Source code file: invblock.c, line: 79 Fatal err

Re: [gmx-users] Re: LINCS metal-ligand bonds

, 2012 at 8:26 PM, Justin Lemkul wrote: > > > On 10/12/12 10:39 AM, Dr. Vitaly Chaban wrote: >>> >>> >>> On 10/12/12 2:42 AM, tarak karmakar wrote: >>>> >>>> Dear ALL, >>>> >>>> In my protein I need to constr

Re: [gmx-users] tyrosyl radical force field

2 at 2:01 PM, Justin Lemkul wrote: >> >> >> On 10/3/12 7:49 AM, tarak karmakar wrote: >>> >>> Thanks Justin, >>> Actually if I would remove the proton from the tyrosine -OH and add >>> the corresponding charge of the Hydrogen to the phenolic oxyge

Re: [gmx-users] tyrosyl radical force field

kul wrote: > > > On 10/3/12 6:00 AM, tarak karmakar wrote: >> >> Dear All, >> >> Is it possible to deal a protein with tyrosyl radical in Molecular >> Dynamics Simulation ?? If possible can you please provide me the >> reference or literature where I can

Re: [gmx-users] specific dihedral plotting

Thanks Mark , I got it now :) On Thu, Sep 20, 2012 at 3:06 PM, Mark Abraham wrote: > On 20/09/2012 7:31 PM, tarak karmakar wrote: >> >> Dear All, >> >>I need to plot a specific dihedral in my protein and I have to >> see how it is changing with

Re: [gmx-users] distance calculation

thanks a lot Mark On Thu, Sep 20, 2012 at 12:31 PM, Mark Abraham wrote: > On 20/09/2012 4:21 PM, tarak karmakar wrote: >> >> Thanks Mark. >> I was using the following command as I got it in the manual. >> g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg >

Re: [gmx-users] distance calculation

) and atom no. 879 (ligand atom) with respect to time) On Thu, Sep 20, 2012 at 10:20 AM, Mark Abraham wrote: > On 20/09/2012 2:05 PM, tarak karmakar wrote: >> >> Thanks Justin. >> >> But in my case I want to plot the distance between one atom in the >> backb

Re: [gmx-users] distance calculation

; > On 9/19/12 2:55 PM, tarak karmakar wrote: >> >> Dear All, >> >> I want to calculate the distance between the nitrogen atom present in >> the ligand and the H- attached to the backbone of the protein along a >> long trajectory. So can anyone suggest me ho

[gmx-users] distance calculation

Dear All, I want to calculate the distance between the nitrogen atom present in the ligand and the H- attached to the backbone of the protein along a long trajectory. So can anyone suggest me how to consider these two atoms to calculate and plot the distance along with the time ? -- Tarak -- gm

Re: [gmx-users] charge calculation........

> On 17/09/2012 10:01 PM, tarak karmakar wrote: >> >> Dear All, >> >> I want to have one of tyrosine residues in my protein to >> be unprotonated. I am using amber force field for the simulation. But >> in aminoacid.rtp there is no entry for the un

[gmx-users] charge calculation........

Dear All, I want to have one of tyrosine residues in my protein to be unprotonated. I am using amber force field for the simulation. But in aminoacid.rtp there is no entry for the unprotonated one. So I am adding it by myself in to the .rtp file. Now I am bit confused with the charge

Re: [gmx-users] extra Oxygen ....upon modification of middle residue

Thanks a lot Justin. On Wed, Aug 29, 2012 at 11:57 PM, Justin Lemkul wrote: > > > On 8/29/12 2:19 PM, tarak karmakar wrote: >> >> Dear All, >> >> In my protein pdb file I am changing the protonation state of residue >> and giving some other name to i

[gmx-users] extra Oxygen ....upon modification of middle residue

Dear All, In my protein pdb file I am changing the protonation state of residue and giving some other name to it . Now after creating the .gro file I see that the residue present before the modified one has been considered as the C-terminal and it is adding one extra oxygen atom to it. I am givin

[gmx-users] dihedral type equation

Dear All, I am using AMBER94 force-field for my protein. In the original force field paper the dihedral functional form has been given as (V/2)[ 1 + cos(nPhi - gamma)] but in GROMACS(4.5.4) manual I see the (1/2) factor is not there [ eq 4.62]. So is this internally handled in GROMACS or should

Re: [gmx-users] simmulated annealing excess temperature........................

Thanks a lot for the quick reply...probably I have overlooked this point earlier ..now I'm getting it properly On Thu, Aug 16, 2012 at 10:33 PM, Justin Lemkul wrote: > > > On 8/16/12 12:57 PM, tarak karmakar wrote: >> >> Dear All, >

[gmx-users] simmulated annealing excess temperature........................

Dear All, In my simulation I want the temperature of the system to be reached at 300 K only after 3 ps. But after 3ps I see temperature became 402 K. So am I doing any mistake in the '.mdp' file given below? define= -DFLEXIBLE constraints= h-bonds integrator = sd

Re: [gmx-users] PLUMED-GROMACS force constant, angle unit

then why should I multiply by the factor 180/pi ? Can you please make it clear, I gotta confused. Thanks, Tarak On Tue, Aug 14, 2012 at 7:17 PM, David van der Spoel wrote: > On 2012-08-14 14:27, tarak karmakar wrote: >> >> Dear All, >> >> In the manual I see the unit of

Re: [gmx-users] desired no of water molecules

sorry '-maxsol' On Tue, Aug 14, 2012 at 11:24 AM, tarak karmakar wrote: > Oh !! > I got it it is not the -nmol but '-maxmol' > thanks to both of u...:) > > On Tue, Aug 14, 2012 at 10:35 AM, Peter C. Lai wrote: >> hmm. What happens if you try -max

Re: [gmx-users] desired no of water molecules

Oh !! I got it it is not the -nmol but '-maxmol' thanks to both of u...:) On Tue, Aug 14, 2012 at 10:35 AM, Peter C. Lai wrote: > hmm. What happens if you try -maxsol instead of -nmol? > > On 2012-08-14 10:24:18AM +0530, tarak karmakar wrote: >> This is the a

Re: [gmx-users] desired no of water molecules

in the system before adding another 612? > > I don't know how VMD counts waters, but another way is to grep -c for SOL in > the resulting gro file and divide by 3. > > On 2012-08-14 10:07:54AM +0530, tarak karmakar wrote: >> Thanks for the quick reply, I have given thi

Re: [gmx-users] desired no of water molecules

)Segments: 1 Info)Fragments: 669 Protein: 1 Nucleic: 0 On Tue, Aug 14, 2012 at 9:46 AM, Mark Abraham wrote: > On 14/08/2012 2:02 PM, tarak karmakar wrote: >> >> Dear All, >> >> Is there any way to add a specific number of water ( let say 650 >> water) molecul

[gmx-users] desired no of water molecules

Dear All, Is there any way to add a specific number of water ( let say 650 water) molecules while dissolving the solute in a given box ? Thanks, Tarak -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! *

Re: [gmx-users] simmulated annealing

Hi Mark, I have used the following .mdp file for the run and got the excess temperature for the system; it has reached the desired temp at around 150-155 ps. But I need to reach the temp at after 300 ps. Thanks, define = -DFLEXIBLE constraints= h-bonds integrator

[gmx-users] simmulated annealing

Dear All, I did the simmulated annealing for a protein where I wanted to increase the temperature from 0 K to 300 K after 300 ps. But after the simulation run I see the temp got increased up to 400 K and so. So can anyone tell me whether I am doing any mistake ? The .mdp file for the run is as fol

[gmx-users] dihedral as CV in Umbrella Sampling

Dear All, I am studying a molecule which is changing its conformation during a reaction. So I want to calculate free energy for the conformational change. I am planning to do Umbrella sampling for this purpose. But what is the way to handle the dihedral angle as a Collective Variable (C

[gmx-users] dihedral as Collective Variable in Umbrella Sampling

Dear All, I am studying a molecule which is changing its conformation during a reaction. So I want to calculate free energy for the conformational change. I am planning to do Umbrella sampling for this purpose. But what is the way to handle the dihedral angle as a Collective Variable (C

Re: [gmx-users] RMSD plot

brium value. Is that because my system is not minimized / equilibrated properly ? Any suggestion ? Thanks On Mon, Jul 30, 2012 at 7:33 AM, Mark Abraham wrote: > On 30/07/2012 3:39 AM, tarak karmakar wrote: >> >> Dear All, >> >> In my initial protein pdb structure I

Re: [gmx-users] About pdb2gmx

see its not a big issue. Look at the atom types of the particular RESIDUE in the pdb file and also have a look into the atom types present in the rtp file. Now if these are matching properly then you can choose any convenient name for that particular residue in the rtp file. But the name of the par

[gmx-users] RMSD plot

Dear All, In my initial protein pdb structure I have added some external ligand molecules and as a result of that there are several short contacts. So, well, I minimized the system and then got the 'prot_min.gro' file. Now after the equilibration run, I plotted the RMSD of the resulting trajectory

[gmx-users] DPOSRE not restraining

Dear All , I wanted to keep all the molecules other than water fixed [ positiion restraints]. So for that I have performed short NVT [simulation with DEPOSRE] after minimization, but while seeing the movie of the trajectory in VMD I see the protein backbone is moving. So did I miss somethi

[gmx-users] metal ligand bond

Dear All, The protein with which I'm working with, contains Zn metal and it has tetrahedral coordination site. There are HISTIDINE side chains within distance ~ 2.3 to 2.4 . So my questions are as follows (1) In that distance range there is no possibility to form a covalent bond between Zn and

[gmx-users] minimization force criteria

Dear All, While running minimization I imposed the the condition for the minimization as to be converged only at Fmax < 10 . But I got the following Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 10 Double precision normally

Re: [gmx-users] Re: angle constraints

ou are attempting to hold these >>>> >> atoms >>>> >>in >>>> >>a straight line I would suggest that a type 2 virtual site might >>>> >>(depending >>>> >>on your system) be a better idea. >>> >>> > >>> > >>>

Re: [gmx-users] angle constraints

Indeed, a much better idea. > > Mark > > >> >> Richard >> >> >> On 24/07/2012 07:21, "tarak karmakar" wrote: >> >>> Oh ! Thnaks >>> I saw that table, the angle_restrain option is there but not constraints >>> . >>

Re: [gmx-users] angle constraints

many times but didn't get proper clue; in one of those mails I saw someone has dealt with some dummy atoms. I could not able to digest that logic. On Tue, Jul 24, 2012 at 11:01 AM, Mark Abraham wrote: > On 24/07/2012 3:21 PM, tarak karmakar wrote: >> >> Dear All, >> &

[gmx-users] angle constraints

Dear All, I am constraining one angle in my protein sample by incorporating " [ constraints ]" block in topology file as [ constraints ] ; index1 index2 index3 funct angle 6064 6063 6065 1 180.0 while doing that its showing the following error Program grompp, VERSION 4.5.5 Sou

[gmx-users] constraints algorithm

ees] maximum angle that a bond can rotate before LINCS will complain -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit JNCASR -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are

Re: [gmx-users] distance_restraints with flexible angle

Exactly so. But in the ffbonded.itp file there are two columns, equilibrium bond length and Kb . So evenif I give zero then it won't affect the bond . Thanks a lot for the reply, it's working fine now . On Mon, Jul 23, 2012 at 6:02 PM, Justin Lemkul wrote: > > > On 7/23/12 8:31

Re: [gmx-users] distance_restraints with flexible angle

Thanks for the reply. But then what should I give as Kb [ bond stretching constant ] in the ffbonded.itp file ? should I give 00.000 there or something else ??? On Mon, Jul 23, 2012 at 4:11 PM, Justin Lemkul wrote: > > > On 7/23/12 2:39 AM, tarak karmakar wrote: >> >> Dear A

[gmx-users] distance_restraints with flexible angle

ogy for ions #include "./amber94.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Other_chain_A 1 SOL 622 -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit JNCASR -- gmx-users mailing listg

[gmx-users] Simulation Box type

I need to have, prior to the simulation. Thanks in advance, Tarak -- Tarak Karmakar Molecular Simulation Lab. C.P.M.U JNCASR -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please se

[gmx-users] pH and protein

particular pH ? [ Protein Calculator !! ] Thanks in advance. -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- gmx-users mailing

Re: [gmx-users] force field parametrs for Mn2+

sorry it's my mistake . thanks a lot for the reply. On Mon, Jul 9, 2012 at 10:55 PM, Justin A. Lemkul wrote: > > > On 7/9/12 1:21 PM, tarak karmakar wrote: >> >> Oh !! nice work >> Thanks a lot for the quick reply. But I'm very sorry to inform you &

Re: [gmx-users] force field parametrs for Mn2+

ibrary.wiley.com/doi/10.1002/anie.201202032/abstract > > > hope it helps > > > > On 07/09/2012 12:21 PM, tarak karmakar wrote: >> >> Dear All, >> >> >> Please suggest me any paper/article that contains force field >> parameters for Mn 2+ . >&

[gmx-users] force field parametrs for Mn2+

Dear All, Please suggest me any paper/article that contains force field parameters for Mn 2+ . Thanks -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA

[gmx-users] simulation box shape and length

be highly appreciated.* * Thanks Tarak -- *Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 * -- gmx-users mailing listgmx

Re: [gmx-users] current directory files

Thanks a lotnow it's working:) On Fri, Jun 15, 2012 at 2:00 PM, Mark Abraham wrote: > On 15/06/2012 6:21 PM, tarak karmakar wrote: > > Hi, > > Thanks for the reply. > One thing, while giving the '-ff' flag it is asking for some string. So I >

Re: [gmx-users] current directory files

> On 15/06/2012 4:27 PM, tarak karmakar wrote: > > Dear All, > > > In my protein pdb file I have changed some of the amino acid residue > names. So accordingly I have changed corresponding residue names in force > filed files and kept all the files [ modified and unmo

[gmx-users] current directory files

) aminoacids.rtp 3) ffnonbonded.itp 4) ffbonded.itp 5) spc.itp 6) ions.itp now while giving the command pdb2gmx -f prot.pdb -o prot.gro -p toplogy.top how can I make use of all these force field files present in my current working directory ? Thanks in advance. -- *Tarak Karmakar Molecular

Re: [gmx-users] pdb2gmx error

; http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- *Tar

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