[gmx-users] Water molecules fill in gaps in protein

Dear Gromacs Users, I noticed that quite often after adding the solvent (water) to the protein, the water molecules fill in gaps inside the protein which are not occupied. I am afraid that since their position may not be optimal (they actually should not be there), it will lead to artifacts as

[gmx-users] Solvent is added inconsistently

Dear All, I am facing an issue I do not fully understand. Namely, let's take two crystallographic structures of the same protein and in one of them let's delete three crystallographic water molecules that are not buried inside the protein (let's forget about a reason for it for a moment). Now,

[gmx-users] Non-bonded interactions settings using Amber

Dear All, I am using amber99fb-star-ildn with Gromacs2016.3 and I'm not sure how to choose some options for non-bonded interactions such as vdw-modifier (potential-shift or potential-shift-verlet or potential-switch) dispcorr (EnerPres or no) rcoulomb rvdw I read original papers about

[gmx-users] Not all snapshots are written to trr during minimization

Dear All, I noticed that after my minimization run I have less snapshots in trr than I expected. For instance, the structure is written every 126-127 steps (plus the last one) even though my mdp file states nstxout = 100 Best wishes, Dawid Grabarek -- Gromacs Users mailing list *

Re: [gmx-users] Change forcefield directory

Dear Justin, I was talking about changing GMXLIB, because she has to transfer her force field files to a different directory than Gromacs is installed in. I am in the same situation and what I did was to copy a whole gromacs-2016.4/share/top directory to my home and changed GMXLIB for this

Re: [gmx-users] Change forcefield directory

Hi, You need to set the GMXLIB to directory with a modified forcefield. Just copy all other files apart from aminoacids.rtp to a new directory with a forcefield. Also, if you want to be sure that you use a correct force field, you can modify first line of forcefield.doc file into something like

Re: [gmx-users] Continuation = yes keyword

rain the > configuration it is supplied, assuming that no constraints have yet been > solved since it is a new run. If the coordinates supplied are from a > previous simulation with constraints, then you are likely going to > change them slightly, thus introducing a discontinuity. >

[gmx-users] Continuation = yes keyword

Dear All, I start my MD simulation from a previous run using data in tpr and cpt files with changed mdp options for the new simulation. Is it really important to use "continuation = yes" for the lincs constraints. What can be wrong if I don't (I use continuation = no). Best wishes, Dawid

Re: [gmx-users] Purpose of repeated improper dihedrals

OK, I see. Thanks again! pt., 2 sie 2019 o 17:07 Justin Lemkul napisał(a): > > > On 8/2/19 8:59 AM, Dawid das wrote: > > Thank you for an asnwer. However, I still need to ask more. > > So, let's take this time the > > NR1 CPH1 CPH2 H > > NR1 CPH2 CPH1 H &

Re: [gmx-users] Purpose of repeated improper dihedrals

. The only reason I see is to make it more rigid because I have "doubled" improper. Best regards, Dawid Grabarek pt., 2 sie 2019 o 13:40 Justin Lemkul napisał(a): > > > On 8/2/19 2:38 AM, Dawid das wrote: > > Dear All, > > > > Why some of the improper p

[gmx-users] Purpose of repeated improper dihedrals

Dear All, Why some of the improper parameters in CHARMM27 FF are repeated with the middle atom types in a different order as in, e.g. HR1 NR1 NR2 CPH22 0. 4.184 HR1 NR2 NR1 CPH22 0. 4.184 while some are not, e.g. HR3 CPH1NR3 CPH1

[gmx-users] Improper dihedral parameters for peptide bond

Dear All, I would like to make sure whether these parameters O X X C 2 0. 1004.16 NH1 X X H 2 0. 167.36 under [ dihedraltypes ] card in ffbonded.itp file are the improper dihedral parameters for the peptide bonds as defined in

[gmx-users] Improper dihedral parameters for peptide bond

Dear All, I would like to make sure whether these parameters O X X C 2 0. 1004.16 NH1 X X H 2 0. 167.36 under [ dihedraltypes ] card in ffbonded.itp file are the improper dihedral parameters for the peptide bonds as defined in

Re: [gmx-users] All water molecules inside protein

Thank you. niedz., 3 lut 2019 o 11:47 David van der Spoel napisał(a): > Den 2019-02-03 kl. 11:09, skrev Dawid das: > > Dear Gromacs Users, > > > > I need to extract gro or pdb file with single snapshot from a trajectory > > for a protein inside solvation box. In the o

[gmx-users] All water molecules inside protein

Dear Gromacs Users, I need to extract gro or pdb file with single snapshot from a trajectory for a protein inside solvation box. In the output, I need whole protein structure + all water molecules "inside" the protein. That could also mean all water molecules within let's say 0.3 nm distance from

Re: [gmx-users] Writing PDB file so that protonation state of HIS is explicit by name

:18 GMT+02:00 Justin Lemkul <jalem...@vt.edu>: > > > On 4/23/18 11:15 AM, Dawid das wrote: > >> Dear All, >> >> Is it possible to create PDB file from XTC so that naming of histidine >> residues >> is HSE, HSD, HSP instead of HIS? >> > &

[gmx-users] Writing PDB file so that protonation state of HIS is explicit by name

Dear All, Is it possible to create PDB file from XTC so that naming of histidine residues is HSE, HSD, HSP instead of HIS? Best wishes, Dawid Grabarek -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] trjconv ndec not working

The quick and dirty solution is that I write gro and g96 and copy coordinates from the latter to the former, but I'd rather have more elaborate solution. 2018-04-18 14:53 GMT+02:00 Dawid das <add...@googlemail.com>: > Dear All, > > I have similar issue. I have created xtc file

Re: [gmx-users] trjconv ndec not working

Dear All, I have similar issue. I have created xtc file with precision of 1.0e-6 nm and I want my gro file to have the same precision, and I get this at the end of trjconv Reading frame 0 time3.000 Precision of npt-md-prod.xtc is 1e-06 (nm) Setting output precision to 1e-06 (nm) Last

Re: [gmx-users] Domain decomposition error

3.5 nm from the side-chain carbon... Sorry for bothering. Best wishes, Dawid 2018-04-15 16:41 GMT+02:00 Justin Lemkul <jalem...@vt.edu>: > > > On 4/15/18 9:29 AM, Dawid das wrote: > >> Dear Gromacs Users, >> >> I run numerous MD simulations for sim

[gmx-users] Domain decomposition error

Dear Gromacs Users, I run numerous MD simulations for similar systems of protein in water box and for only one system I encounter error: *Fatal error:There is no domain decomposition for 4 ranks that is compatible with the givenbox and a minimum cell size of 3.54253 nmChange the number of

[gmx-users] Parameters in top

Dear Gromacs Users, If I have some bonding parameters defined in aminoacids.rtp instead of ffbonded.itp I noticed that these parameters appear in my topology *top file. If I change these parameters in *top file but not in aminoacids.rtp, and get new *trp file with grompp will my parameters also

Re: [gmx-users] How to understand compressed-x-precision?

OK, thank you. 2018-03-24 22:02 GMT+01:00 Mark Abraham <mark.j.abra...@gmail.com>: > Hi, > > That coordinates will have three digits of precision, e.g from multiplying > by 1000, truncating to an integer and dividing by 1000 again. > > Mark > > On Sat, Mar

Re: [gmx-users] Different results from gmx rms

I checked again and it didn't. 2018-03-24 21:58 GMT+01:00 Mark Abraham <mark.j.abra...@gmail.com>: > Hi, > > Did gmx rms warn you suitably that it was making guesses about masses? > > Mark > > On Sat, Mar 24, 2018, 21:07 Dawid das <add...@googlemail.com> wrote

[gmx-users] How to understand compressed-x-precision?

Dear Gromacs Users, As in the topic. How do I understand default precision of 1000 for *compressed-x-precision* option? Best wishes, Dawid Grabarek -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] Different results from gmx rms

definition and plausibly for my new non-hydrogen atoms, the guessed mass is that of carbon, while there are carbon, nitrogen, oxygen atoms. Best regards, Dawid 2018-03-24 20:56 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > On 3/24/18 3:55 PM, Dawid das wrote: > >> Hi,

Re: [gmx-users] Different results from gmx rms

> > On Sat, Mar 24, 2018, 20:32 Dawid das <add...@googlemail.com> wrote: > > > Dear Gromacs Users, > > > > I get a bit different RMS when I use either minimize.tpr or > > start-crystal-structure.gro as a reference structure. > > This is definitely not bec

[gmx-users] Different results from gmx rms

Dear Gromacs Users, I get a bit different RMS when I use either minimize.tpr or start-crystal-structure.gro as a reference structure. This is definitely not because some atoms come across the boundary as simulation progresses (I checked that). What could be the reason? Does minimize.tpr use a

[gmx-users] Position restraints do not work with steepest descent

Dear Gromacs Users, I have used 1000 kJ/(mol*nm^2) or 5000 kJ/(mol*nm^2) force constants for restraining my protein atoms positions during steepest descent minimization and as I watch the "trajectory", the atoms of protein still change their position. The RMSD after 2000 steps is ca. 0.009 nm. Is

Re: [gmx-users] Decrease position restraints force constant on the fly

y, you may able to control the restraint using > plumed. Check the "Moving on a more complex path" in this tutorial ( > https://plumed.github.io/doc-v2.3/user-doc/html/belfast-5.html). > > Ruan > > On Mon, Mar 12, 2018 at 10:38 AM, Justin Lemkul <jalem...@vt.edu> wr

[gmx-users] Decrease position restraints force constant on the fly

Dear Gromacs Users, Is possible to decrease force constant for position restraints as the MD simulation progresses? For instance I start with 1000 kJ/(mol *nm2) and after 20 ps I go to 800 kJ/(mol*nm2), then after 20 ps to 600 kJ/(mol*nm2), etc.? Best wishes, Dawid Grabarek -- Gromacs Users

Re: [gmx-users] Writing pdb snapshot with charge from gro trajectory

a simple > script to (i) parse the topology, (ii) match it with the PDB file, and > (iii) add an extra column at the end of the PDB with the respective > charges. This should be relatively simple to do with your favorite > scripting language. > > Cheers, > J > > On Wed, Nov 8,

[gmx-users] Writing pdb snapshot with charge from gro trajectory

Dear Gromacs Users, I have a trajectory of my MD simulation in *.gro format. Is it possible to write the pdb snapshot from the trajectory so that the pdb file contains the atomic charge from top file? The charge should be put at the end of my pdb file. Best wishes, Dawid Grabarek -- Gromacs

Re: [gmx-users] How to obtain a proper structure for glycine?

Oh, I'm sorry for misleading you. You need use -ter The -noter means that you DON'T want to choose protonation yourself. Give this one a try. 2017-08-06 20:38 GMT+02:00 ZHANG Cheng <272699...@qq.com>: > Hi Dawid, > Thank you. However, I still got three hydrogens after running: > > > gmx

Re: [gmx-users] How to obtain a proper structure for glycine?

Hi Cheng, By default, the termini of a polypeptide are charged. You need option -noter in your gmx pdb2gmx command to interactively tell it what charge (no charge in your case) you want for your termini. Best wishes, Dawid 2017-08-06 20:20 GMT+02:00 ZHANG Cheng <272699...@qq.com>: > Hi Mark,

[gmx-users] Calculate RMSD between snapshots of two trajectories

Dear Gromacs Users, I would like to get a simple plot of RMSD versus time for two trajectories in *.gro format, where RMSD is calculated between structures at the same time, i.e. snap11 - snap12 snap21 - snap22 snap31 - snap32 snap41 - snap42 . . . where snap31 means third snapshot of the first

Re: [gmx-users] gmx check

use of > "correct" is in the sense of "between sensible atom indices" rather than > suggesting that only one length is valid. > > Mark > > On Fri, 28 Jul 2017 14:41 Dawid das <add...@googlemail.com> wrote: > > > Hi, > > > > No,

Re: [gmx-users] gmx check

-07-28 13:33 GMT+02:00 Mark Abraham <mark.j.abra...@gmail.com>: > Hi, > > It's hard to tell without seeing the messages and knowing whether those > bonds were constrained. > > Mark > > On Fri, 28 Jul 2017 13:19 Dawid das <add...@googlemail.com> wrote: > > &

[gmx-users] gmx check

Dear Gromacs Users, I get a bunch of communicates when I run gmx check -f npt-md2.xtc -s1 npt-md2.tpr >& gmx-check2.out saying that I get different bond lengths than they should be. Can that be caused by only 0.001 nm precision of my results? Also I am not exactly sure if I understand correctly

Re: [gmx-users] Significance of box vectors in GRO trajectory file.

By the way, why does this vector change during simulation? What if I use >> exactly the same vector for my whole >> simulation? >> >> > This is the function of pressure coupling. If you keep the box vectors > fixed, that is an NVT simulation. Aaaah, very well then. Thank you for explaining

Re: [gmx-users] Significance of box vectors in GRO trajectory file.

lem...@vt.edu>: > > > On 6/5/17 10:07 AM, Dawid das wrote: > >> Dear Gromacs Users, >> >> Suppose I have a trajectory file in gro format. If I change the last line >> for each >> snapshot (i.e. line with box vectors values) into an arbitrary set

[gmx-users] Significance of box vectors in GRO trajectory file.

Dear Gromacs Users, Suppose I have a trajectory file in gro format. If I change the last line for each snapshot (i.e. line with box vectors values) into an arbitrary set of three numbers, will it have impact on further manipulations of this gro trajectory file with trjconv? In other words, is

Re: [gmx-users] Group-based cutoff on non-bonded interactions with CHARMM22

? To what extent do I violate the applicability of parameters that were optimized based on a different algorithm? Dawid 2017-05-21 0:30 GMT+02:00 Justin Lemkul <jalem...@vt.edu>: > > > On 5/20/17 8:28 AM, Dawid das wrote: > >> Hi Mark, >> >> Thank you. Actually

Re: [gmx-users] gromacs bond energy calculate

Hi Jane, I don't know if you can do that with one of Gromacs tools, but you can easily extract your bond length/angle values as a function of time with gmx distance and gmx angle, respectively. Then, knowing the formula for bond and angle energies as well as parameters (force constants and

Re: [gmx-users] Group-based cutoff on non-bonded interactions with CHARMM22

re removed > perforce. > > Mark > > On Fri, 19 May 2017 18:44 Dawid das <add...@googlemail.com> wrote: > > > Dear Gromacs Users, > > > > I am a bit confused whether I shouldn't use charge > > group-based cut-off for electrostatics when using CHARMM22. >

[gmx-users] Group-based cutoff on non-bonded interactions with CHARMM22

Dear Gromacs Users, I am a bit confused whether I shouldn't use charge group-based cut-off for electrostatics when using CHARMM22. If I shouldn't use it, what is the purpose of specification of charge groups in original CHARMM files? Best wishes, Dawid -- Gromacs Users mailing list * Please

[gmx-users] 1-4 interactions in CHARMM force field

Dear Gromacs Users, I would like to hear your advice on scaling 1,4-interactions for both classical and QM/MM molecular dynamics simulations. I am using CHARMM27 force field. Firstly, for classical MD, according to this post https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat=1048 I

Re: [gmx-users] Heavy atom - hydrogens bond lengths constraints.

Yes, you are right. This is due to limited precision of xtc file. For trr I don't get the same. I would never expect such large discrepancies. Thank you very much! 2017-05-06 16:33 GMT+02:00 Jochen Hub <j...@gwdg.de>: > > > Am 06.05.17 um 15:35 schrieb Dawid das: > >> Dea

[gmx-users] Heavy atom - hydrogens bond lengths constraints.

Dear Gromacs Users, I am a bit anxious about the results I get for my simulation of protein in a box of water using CHARMM 27 force field. Namely, even though I use following options to constrain bond lengths between hydrogen atoms and heavy atoms: constraint_algorithm= lincs constraints

Re: [gmx-users] Regarding reading .gro file in python

Hello Dilip, I don't really get what your problem is. What do you actually want to do? Read-in and parse a *.gro file which is output from MD simulation? Then for instance, your Python script should calculate something from, e.g. distance between centres of masses of residues of interest? Or do

Re: [gmx-users] converting .gro trajectory to .pdb

Hi, I guess you can try gmx trjconv -f file.gro -o file.pdb -pbc mol -s file.tpr -center 2017-01-18 16:14 GMT+01:00 Irem Altan : > Hi, > > I have a trajectory saved in .gro format. It has multiple frames/snapshots > in it. I’m using .gro format because I needed higher

Re: [gmx-users] Fwd: LJ cut-offs

Since I join this discussion, this is perhaps a good moment to ask following questions. I use Gromacs 5.0.4 and the file.mdp options that I found here http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM , so: 1. The bug that was described here

Re: [gmx-users] Fwd: LJ cut-offs

Also, you could try to find something in these articles: http://apps.webofknowledge.com/Search.do?product=WOS=P2QP4ybhv2TW78yMOMx_mode=GeneralSearch=9bcb8bea-c281-4524-a7de-e664898a322b 2017-01-11 13:48 GMT+01:00 Dawid das <add...@googlemail.com>: > You might also want to read th

Re: [gmx-users] Fwd: LJ cut-offs

Hi, I believe that Mohsen here did not ask about what you are writing about Mark. He asks about cut-offs not the exponents in the LJ formula. I am no expert in that but I reviewed Andrew Leach's book on that and also other resources and I did not find any reason why lower and upper cut-off for

Re: [gmx-users] How the default parameters for PME (particle mesh Ewald) are chosen?

Thank you, now I understand relationship between beta and ewald_rtol :). I will read the article you suggested and let you know if I have further questions. 2017-01-02 19:00 GMT+01:00 Mark Abraham <mark.j.abra...@gmail.com>: > Hi, > > On Mon, Jan 2, 2017 at 6:31 PM

Re: [gmx-users] How the default parameters for PME (particle mesh Ewald) are chosen?

t; On Mon, Jan 2, 2017 at 3:46 PM Dawid das <add...@googlemail.com> wrote: > > > Dear All, > > > > I have at least two questions regarding PME in Gromacs 5.0.4. > > > > Firstly, in my *.log file there is a line that reads > > > > Will do ordinary re

[gmx-users] How the default parameters for PME (particle mesh Ewald) are chosen?

Dear All, I have at least two questions regarding PME in Gromacs 5.0.4. Firstly, in my *.log file there is a line that reads Will do ordinary reciprocal space Ewald sum. Using a Gaussian width (1/beta) of 0.384195 nm for Ewald Is "beta" the relative weight of direct and reciprocal sums? If

Re: [gmx-users] Force field transformation from Gromacs to Charmm format

Thank you! I will definitely have a close look at that. Best regards, Dawid 2016-12-19 2:33 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > On 12/18/16 12:22 PM, Dawid das wrote: > >> Dear All, >> >> Have you ever seen a script/tool that allows for transfor

[gmx-users] Force field transformation from Gromacs to Charmm format

Dear All, Have you ever seen a script/tool that allows for transformation of the Gromacs force field files into CHARMM force field files? I can see that there is a Pythons script that does the other way around. Also I could use a tool that creates *.psf file from *.top file. I googled for that

[gmx-users] Different RMSD plots when either *.gro or *.tpr files are used

Dear Gromacs Experts, I have created two RMSD plots of my protein. For one, as a reference structure source, I have used file.gro and in the other a file.tpr, both from previous calculations. I have obtained slightly different values and i.e. plots. Is that because my reference structures where

Re: [gmx-users] Adding hydrogen atom to specific Glu/Asp carboxyl oxygen atom

dhe...@gmail.com>: > Exchange their atom names？ > > Dading Huang > > On Wed, Nov 9, 2016 at 7:23 PM, Dawid das <add...@googlemail.com> wrote: > > > Dear Gromacs Experts, > > > > I know how to specify which Glu/Asp residues are to be > > protonated/depr

[gmx-users] Adding hydrogen atom to specific Glu/Asp carboxyl oxygen atom

Dear Gromacs Experts, I know how to specify which Glu/Asp residues are to be protonated/deprotonated with pdb2gmx tool. However, I do not like that the hydrogen is added to one of the oxygen atoms of carboxyl moiety. I would like it to be found on the other oxygen. Is there any other way except

Re: [gmx-users] How the angle/bond length changes during simulation.

O'right, I found my mistake. Now it works fine. Thank you! 2016-03-09 16:11 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > On 3/9/16 10:11 AM, Dawid das wrote: > >> 2016-03-09 16:07 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: >> >> >>> Y

Re: [gmx-users] How the angle/bond length changes during simulation.

2016-03-09 16:07 GMT+01:00 Justin Lemkul : > > You are. That's what -all is for: > > "Plot all angles separately in the averages file, in the order of > appearance in the index file." > > Open up angaver.xvg and you will see the average, then the two individual > time series.

[gmx-users] How the angle/bond length changes during simulation.

Dear Gromacs Experts, How can I get a plot of a bond length/ valence angle/ dihedral angle during simulation from *xtc and *.ndx files? I am pretty sure that it is possible, but with g_angle and g_bond I can get only the distribution. By the way, when I use g_angle -f npt-md2-cent.xtc -n

Re: [gmx-users] Different charges in ffnonbonded.itp and aminoacids.rtp files.

Very well. Thank you! 2016-03-06 17:25 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > On 3/6/16 11:17 AM, Dawid das wrote: > >> Dear Gromacs Experts, >> >> Why for some atomtypes the charges are different in ffnonbonded.itp and >> aminoacids.rtp files?

[gmx-users] Different charges in ffnonbonded.itp and aminoacids.rtp files.

Dear Gromacs Experts, Why for some atomtypes the charges are different in ffnonbonded.itp and aminoacids.rtp files? For instance for CD1 CA 0.035 8 from TRP residue the charge for CA type residue is actually -0.115 Does it mean that van der Waals parameters for this CD1 atom of

Re: [gmx-users] Constraining hydrogen - heavy atom bonds with different naming.

Yes of course, but I have already performed a few of simulations. Too bad. I need to repeat them. However, final question. Other atom names can start with M? DG -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] Constraining hydrogen - heavy atom bonds with different naming.

Oh gosh..., so in that case is there any other way around to constraint those MH11 - MCB1 etc. bond lengths except for renaming all hydrogen atoms? Best wishes, Dawid Grabarek 2016-03-01 19:29 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > On 3/1/16 1:24 PM, Dawid das wrote: &g

[gmx-users] Constraining hydrogen - heavy atom bonds with different naming.

Dear Gromacs Experts, I am pretty sure I have already answered this question long time ago but I cannot find it. What I did is I added a new residue for my system and it contains hydrogen atoms. Now, the thing is that all atoms names start with "M", so I have MH21, MH22, MCA1, etc. atoms. I want

[gmx-users] No bonds in *.top file

Dear Gromacs Experts, I run gmx pdb2gmx and it runs without any warnings or errors by the *.top file does not contain any bonds. The *.gro file is fine and all hydrogen atoms are added correctly. Now I have discovered that when I get rid of calcium ions in my *.pdb file I get proper *.top file.

Re: [gmx-users] Atom X in residue YYY was not found in rtp fil

2016-02-27 22:42 GMT+01:00 Justin Lemkul : > Content is read by position, which is precisely your problem. > Yes, I am aware of that. By I did not change anything in position of my *.pdb file. I know that in different years the format changes somehow. The *.pdb file I am using

[gmx-users] Atom X in residue YYY was not found in rtp fil

Dear Gromacs Experts, I have created a new residue for which atom names in my *.pdb file are 4-signs long. When I run gmx pdb2gmx I get following error Fatal error: Atom MCA in residue CH6 65 was not found in rtp entry CH6 with 33 atoms while sorting atoms. I am absolutely one hundred percent

Re: [gmx-users] How the topology file is created based on *.gro file?

k > > On Wed, 3 Feb 2016 10:13 Dawid das <add...@googlemail.com> wrote: > > > Dear Gromacs Experts, > > > > Let's assume that I have a *.gro file in a proper format but the number > of > > atoms and/or > > residues is let's say random, e.g. I have coordin

[gmx-users] How the topology file is created based on *.gro file?

Dear Gromacs Experts, Let's assume that I have a *.gro file in a proper format but the number of atoms and/or residues is let's say random, e.g. I have coordinates of atoms for residue 87, 95, 96, 88. What is more, I have let's say 76 atoms in the system, but I start numbering from 999. Will I be

Re: [gmx-users] How the topology file is created based on *.gro file?

) you can convert your original.gro using editconf and in the final > gro file will be corrected. > > On Wed, Feb 3, 2016 at 11:24 AM Dawid das <add...@googlemail.com> wrote: > > > So it turns out that what is important is the order, i.e. when I want > > connection > > b

Re: [gmx-users] Molecular dynamics with methyl groups instead of peptide bonds.

l.com>: > Hi, > > Generally one would use acetyl or N-methylamine capping groups respectively > for N and C termini of cleaved peptide bonds. These are often called ACE > and NME in .rtp files. > > Mark > > On Tue, Feb 2, 2016 at 2:58 PM Dawid das <add...@goo

[gmx-users] Molecular dynamics with methyl groups instead of peptide bonds.

Dear Gromacs Experts, I would like to perform MD simulation of a system consisting of few amino acids cut out of the protein. The thing is that I break some peptide bonds and I add methyl groups in this place. Now I am missing charmm22 parameters for proper bonds. Could you give me a tip on

[gmx-users] Choose index group from terminal input.

Dear Gromacs Experts, Let's say that for some reasons I don't want to specify the atom group when g_rms (or other module) prompts me to do so. So I do not want to see this: Select group for RMSD calculation Group 0 ( System) has 38387 elements Group 1 (Protein) has 3470

Re: [gmx-users] Choose index group from terminal input.

O'right, I have figured that out myself. Just use text file like data.txt with two lines: 1 1 and redirect it: g_rms [options] < data.txt 2015-09-17 11:32 GMT+01:00 Dawid das <add...@googlemail.com>: > Dear Gromacs Experts, > > Let's say that for some reasons I don't want t

Re: [gmx-users] Choose index group from terminal input.

Thank you. 2015-09-17 12:37 GMT+01:00 Mark Abraham <mark.j.abra...@gmail.com>: > Hi, > > Yes. Further options at > http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts > > Mark > > On Thu, Sep 17, 2015 at 1:04 PM Dawid das <add...@googlemail.

Re: [gmx-users] Accelerating data analysis.

parts of the >> trajectory in parallel, using separate g_rms processes, then concatenating >> the output. Use -b and -e options to limit the analysis to specific >> intervals. >> >> Kind regards, >> Erik >> >> On 15 Sep 2015, at 13:37, Dawid das <add...@

[gmx-users] Accelerating data analysis.

Dear Gromacs Experts, I have an enormous *trr file, which has 1 000 000 points. Now, I know that I can modify this file with trjconv, but let's say I do not want to do it, but I want to have my 1 000 000 points in *xvg file when I use g_rms for instance. Is there a way to accelarate it? Best

Re: [gmx-users] Accelerating data analysis.

te g_rms processes, then concatenating > the output. Use -b and -e options to limit the analysis to specific > intervals. > > Kind regards, > Erik > > > On 15 Sep 2015, at 13:37, Dawid das <add...@googlemail.com> wrote: > > > > Dear Gromacs Experts, > > > &g

Re: [gmx-users] Accelerating data analysis.

ve a > better time implementing Erik's strategy if you break the trajectory into > parts with trjconv, convert it to .xtc, or write it as .xtc in the first > place. See also > > http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume > > Mark > > O

Re: [gmx-users] Accelerating data analysis.

hat what I should expect? 2015-09-15 13:45 GMT+01:00 Dawid das <add...@googlemail.com>: > Dear All, > > Thank you all. Especially for your tip Erik ;). > > Dawid > > 2015-09-15 13:42 GMT+01:00 Erik Marklund <erik.markl...@chem.ox.ac.uk>: > >> Dear Dawi

Re: [gmx-users] question

Dear Atila, I am no specialist but in general all force fields are designed to recover specific properties. So that other can give you more tips, tell us what your aim is. Why do you want to simulate RNA and what properties or phenomena are you interested in? Best wishes, Dawid Grabarek

Re: [gmx-users] Heating step by step.

, grompp says: Fatal error: Not enough annealing values: 1 (for 2 groups) I believe I do everything according to the documentation. 2015-09-04 22:41 GMT+01:00 Dawid das <add...@googlemail.com>: > > 2015-09-04 22:03 GMT+01:00 Vitaly V. Chaban <vvcha...@gmail.com>: > >&g

Re: [gmx-users] Heating step by step.

Justin Lemkul <jalem...@vt.edu>: > > > On 9/5/15 5:48 AM, Dawid das wrote: > >> I struggle to properly define my *mdp file. I have following keywords and >> their values: >> >> ;Simulated annealing is on >> annealing = single >> annealin

Re: [gmx-users] Heating step by step.

O'right, it seems that I did everything correctly. Thank you for your help! :) 2015-09-05 14:30 GMT+01:00 Dawid das <add...@googlemail.com>: > Yes, that is right Justin. But I still need: > tcoupl = V-rescale ; modified Berendsen thermostat > tc-grps

Re: [gmx-users] CMAP missing for a new residue.

It seems to work :). Thank you! 2015-09-04 9:52 GMT+01:00 Dawid das <add...@googlemail.com>: > > 2015-09-03 13:06 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > >> FYI, CHARMM22 has no CMAP. CHARMM22/CMAP (what GROMACS somewhat >> misleadingly calls "cha

[gmx-users] Heating step by step.

Dear Gromacs Experts, Is it possible to do following heating of my system: increase reference temperature by 20 K every 5 ps of simulation in one run until I reach 300 K? According to what I found in one of papers, it is possible to do with NAMD. Best wishes, Dawid Grabarek -- Gromacs Users

Re: [gmx-users] Heating step by step.

2015-09-04 22:03 GMT+01:00 Vitaly V. Chaban : > However, your simulation schedule makes little sense physically . > What do you mean by that? I just want to heat up my system gently before equilibration phase. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] CMAP missing for a new residue.

2015-09-03 13:06 GMT+01:00 Justin Lemkul : > FYI, CHARMM22 has no CMAP. CHARMM22/CMAP (what GROMACS somewhat > misleadingly calls "charmm27.ff") does. > Yes, I was aware of that, just forgot to write CHARM22/CMAP. > > My question is, whether there is a way to use CMAP

[gmx-users] CMAP missing for a new residue.

Dear Gromacs Experts, I am working with fluorescent protein, posesing a chromophore which I defined as a non-standard " amino-acid residue". Now, I want to use Charmm22 force field and the issue is that I am missing CMAP parameters and these are not available in the literature. My question is,

[gmx-users] How error estimate is calculated by g_energy?

Dear Gromacs experts, Although I have read both online and printed Gromacs manual I am still not sure how the error estimate value is calculated when I use g_energy and choose pressure or density for instance. Could you explain it in simple words? Best wishes, Dawid Grabarek -- Gromacs Users

Re: [gmx-users] None constraints and l-bfgs.

that your approach will trigger? Mark On Sun, 9 Aug 2015 19:42 Dawid das add...@googlemail.com wrote: 2015-08-09 18:27 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: Justin's advice is true only if your water topology has a flexible implementation. Check it Yes, I do use

Re: [gmx-users] None constraints and l-bfgs.

at 10:30 AM Dawid das add...@googlemail.com wrote: Well, the *itp file says: #ifdef FLEXIBLE and there is bunch of lines defining proper parameters, so I assumed this is it. 2015-08-10 6:26 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: You've *tried* to use flexible water

Re: [gmx-users] None constraints and l-bfgs.

2015-08-09 18:25 GMT+01:00 Justin Lemkul jalem...@vt.edu: Are you using some old version? Note that your cutoff setup is wrong for CHARMM force fields. Well, to be honest I do use quite and old version which is 4.6.7. Yes I am aware of that I use wrong CHARMM force field cutoff setup and

Re: [gmx-users] None constraints and l-bfgs.

2015-08-09 18:27 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: Justin's advice is true only if your water topology has a flexible implementation. Check it Yes, I do use flexible water and still this causes problem. -- Gromacs Users mailing list * Please search the archive at

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