[gmx-users] velocity

Dear Mark, Thanks for your answer. "Only if you asked for velocity information to be written to the trajectory, with nstvout" Usually, I use the following lines in mdp files: nstxout = 1000 nstvout = 1000 nstxtcout = 1000 nstenergy = 1000 nstlog = 1000 But, I get only position of atoms

[gmx-users] velocity

Dear Justin, In my last md simulation, I used nstxout = 1000 nstvout = 1000 nstxtcout = 1000 nstenergy = 1000 nstlog = 1000 After your suggestion, I used gmx traj -f npt.xtc -s npt.tpr -ov veloc.xvg -n index.ndx veloc.xvg file is as follows:

[gmx-users] md simulation of oil hydrocarbon

Hi all, I want to do md simulation of oil hydrocarbon? Is there appropriate force field for these hydrocarbons in gromacs? What I see in gromacs force fields only was related to aminoacids and nucleotides. What is your suggestion for md simulation of oil hydrocarbon? Best, -- Gromacs Users

Re: [gmx-users] md simulation of oil hydrocarbon

for liquids use oplsaa On Mon, May 28, 2018 at 12:23 PM, Atila Petrosian wrote: > Hi all, > > I want to do md simulation of oil hydrocarbon? > > Is there appropriate force field for these hydrocarbons in gromacs? > > What I see in gromacs force fields only was related to aminoacids and >

Re: [gmx-users] velocity

Maybe you checked .xtc file Velocity is in .trr file Quyen V. Vu Web frontend developer On Mon, May 28, 2018, 18:42 Mark Abraham wrote: > Hi, > > Only if you asked for velocity information to be written to the trajectory, > with nstvout > > Mark > > On Mon, May 28, 2018 at 1:06 PM Atila

Re: [gmx-users] AMP_simulation

The ATB generator does a reasonable job, but for some reason it gets some things wrong. If you can look at that topology, identify the problematic parts of it, see if that is consistent with the forcefield, and then if not adjust the parameters. Particularly I have found that some angles are way

Re: [gmx-users] Regarding calculation of SDF

What exactly is the issue? It isn't clear what the problem is; the fact it is having trouble with using the tng file format, or the output in the cube file that is then loaded into vmd? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical

Re: [gmx-users] QM-MM (sai manohar)

Thank you for the guidance. I shall browse through for other alternatives. :) On Mon, May 28, 2018 at 6:14 PM, Groenhof, Gerrit wrote: > Hi, > > Unfortunately, for this to work > you need to have both heme and protein in one topology. > > best, > > gerrit > > Tidings and a good day. > > Hi, >

[gmx-users] velocity

Dear Mark and Justin, My problem was solved using trr file. Thanks for guidance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For

[gmx-users] md simulation of oil hydrocarbon?

Hi all, I want to do md simulation of oil hydrocarbon? Is there appropriate force field for these hydrocarbons in gromacs? Is it possible with gromacs? Best, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] calculation of distance between the center of geometry of two proteins

hi, to calculate the distance between the center of geometry of two proteins, i am using this command g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg -select 'cog of group "Chain_A" plus cog of group "Chain_B"' Invalid command line argument: -select here in this index file

Re: [gmx-users] calculation of distance between the center of geometry of two proteins

after deleting -select this error is coming Invalid command line argument: cog of group "Chain_A" plus cog of group "Chain_B" On 5/28/18, Soham Sarkar wrote: > Delete from -select.. previous are ok > > On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM,

Re: [gmx-users] calculation of distance between the center of geometry of two proteins

Hi, g_dist does not take selection arguments so you cannot use -select or anything that was an argument to it. You can either rely on the default selections that all GROMACS tools make if there is no index file, or use e.g. g_select to make an index file with the selections you want. Note that

[gmx-users] velocity

Dear gromacs users, I did md simulation. I need to velocity values for each atoms in time steps. Can I get this parameter from trajectory file directly? How to obtain that? Thanks -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] calculation of distance between the center of geometry of two proteins

thank you so much for your reply. On 5/28/18, Soham Sarkar wrote: > use the latest .tpr formed after production run else try > > tpbconv -s dynamic.tpr -o dynamic_new.tpr > > On Mon, May 28, 2018 at 3:29 PM, SHAHEE ISLAM > wrote: > >> thank you so

Re: [gmx-users] calculation of distance between the center of geometry of two proteins

The command should be g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg Then select Chain_A and Chain_B as per the indexing number On Mon, May 28, 2018 at 3:24 PM, SHAHEE ISLAM wrote: > after deleting -select > this error is coming > Invalid command

[gmx-users] QM-MM

Tidings and a good day. Hi, I'm looking at a QM-MM/Gromacs optimization for a Heme-CYP system. How do I take it forward. I've found one strategy using a dummy atom in linker. However, there's a small issue in this route. How do we incorporate the dummy if the link we are pursuing is between the

Re: [gmx-users] velocity

Hi, Only if you asked for velocity information to be written to the trajectory, with nstvout Mark On Mon, May 28, 2018 at 1:06 PM Atila Petrosian wrote: > Dear gromacs users, > > I did md simulation. I need to velocity values for each atoms in time > steps. > > Can

Re: [gmx-users] calculation of distance between the center of geometry of two proteins

Delete from -select.. previous are ok On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, wrote: > hi, > to calculate the distance between the center of geometry of two > proteins, i am using this command > g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg >

Re: [gmx-users] calculation of distance between the center of geometry of two proteins

thank you so much. after deleting from -select its now working.but the fatal error is Molecule in topology has atom numbers below and above natoms (565). You are probably trying to use a trajectory which does not match the first 565 atoms of the run input file. You can make a matching run input

Re: [gmx-users] calculation of distance between the center of geometry of two proteins

use the latest .tpr formed after production run else try tpbconv -s dynamic.tpr -o dynamic_new.tpr On Mon, May 28, 2018 at 3:29 PM, SHAHEE ISLAM wrote: > thank you so much. > after deleting from -select its now working.but the fatal error is > Molecule in topology has

Re: [gmx-users] QM-MM (sai manohar)

Hi, Unfortunately, for this to work you need to have both heme and protein in one topology. best, gerrit Tidings and a good day. Hi, I'm looking at a QM-MM/Gromacs optimization for a Heme-CYP system. How do I take it forward. I've found one strategy using a dummy atom in linker. However,

Re: [gmx-users] velocity

Hi, An xtc file only contains positions. Your nstvout affects the trr file. Notice how sharing your command line got you the answer you needed ;-) Mark On Mon, May 28, 2018, 18:12 Atila Petrosian wrote: > Dear Justin, > > In my last md simulation, I used > > nstxout

[gmx-users] (no subject)

Hello, Can anyone provide me the topology for Adenosine Monophosphate Molecule (AMP)for Gromacs (gromos54a7 forcefield). Thanks Nikita Bora * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named

[gmx-users] Partial Charge precision

Hello, how many decimal digits are allowed in .rtp files for partial charges? i got this error: ## Using the Uff4mof force field in directory ./uff4mof.ff No file 'watermodels.dat' found, will not include a water model Reading benzene.pdb... Read

Re: [gmx-users] Partial Charge precision

On 5/28/18 10:34 AM, Momin Ahmad wrote: Hello, how many decimal digits are allowed in .rtp files for partial charges? i got this error: ## Using the Uff4mof force field in directory ./uff4mof.ff No file 'watermodels.dat' found, will not include a

Re: [gmx-users] Partial Charge precision

Hi, yeah i missed the charge group number. Thanks for reminding Cheers, Momin Am 28.05.2018 um 16:59 schrieb Justin Lemkul: On 5/28/18 10:34 AM, Momin Ahmad wrote: Hello, how many decimal digits are allowed in .rtp files for partial charges? i got this error:

Re: [gmx-users] velocity

On 5/28/18 11:49 AM, Atila Petrosian wrote: Dear Mark, Thanks for your answer. "Only if you asked for velocity information to be written to the trajectory, with nstvout" Usually, I use the following lines in mdp files: nstxout = 1000 nstvout = 1000 nstxtcout = 1000 nstenergy = 1000

[gmx-users] g_sas

Dear Gromacs users, I want to calculate the hydrophobic and hydrophilic area of a protein by using the g_sas command. I have used: g_sas -f md.xtc -s md.tpr -o area.xvg -tv volume.xvg However, looking at the area.xvg with xmgrace, I can only see the hydrophobic area not the hydrophilic.

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 169, Issue 96

> Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body

Re: [gmx-users] g_sas

Dear Cristina, how did you call xmgrace? Did you supply the "-nxy" switch before area.xvg or volume.xvg? Regards, Andras On 05/28/2018 09:45 AM, Gonzalez Fernandez, Cristina wrote: > Dear Gromacs users, > > > > > > I want to calculate the hydrophobic and hydrophilic area of a protein by >

[gmx-users] D Gsolv

Dear Gromacs users, Does anyone know the meaning of "D Gsolv" when you plot the area.xvg (output of g_sas)? Any help will highly been appreciated. Best, C. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] Colchicine topology

That's not my intention - someone seeking a topology would do well to a) know the past research to inform their decisions, including whether to repeat deliberately, and b) also ask them to share input files. I was obviously joking, not to derail this thread. Besides, in biomolecular fields,

[gmx-users] Solvation of the bilayer

Dear Gromacs users, I have a bilayer in xy plane. I tried to solvate the bilayer (sur_bilayer.pdb) with water molecules using gmx solvate. I used the command; gmx solvate -cp sur_bilayer.pdb -maxsol 28197 -o sur_water_bilayer.pdb However, water molecules are not distributed in the hydrophilic

Re: [gmx-users] Solvation of the bilayer

What are the dimensions of your bilayer and your box, and where do the water molecules go? On 5/28/2018 12:20 AM, Amali Guruge wrote: Dear Gromacs users, I have a bilayer in xy plane. I tried to solvate the bilayer (sur_bilayer.pdb) with water molecules using gmx solvate. I used the command;

Re: [gmx-users] Colchicine topology

Hi, I found a couple of papers doing MD on colchicine and tubulin in a few minutes on Google - maybe you should start there and also check your work will be novel :-) Mark On Sat, May 26, 2018 at 8:00 AM Harutyun Sahakyan wrote: > Hi all, > > > > I use gromacs for MD

Re: [gmx-users] Colchicine topology

Mark, please don't be one of those people telling young researchers that everything has already been done. :) My postdoc (a fellow, actually -- with her own project & funding) is reading all these horrible papers and, according to her, everything has been done. Drives me nuts! Alex On

Re: [gmx-users] Colchicine topology

Hi, On Mon, May 28, 2018 at 9:17 AM Alex wrote: > Mark, please don't be one of those people telling young researchers that > everything has already been done. :) > That's not my intention - someone seeking a topology would do well to a) know the past research to inform

Re: [gmx-users] Colchicine topology

Dear All, I have a simulation box of dimension 8*6*4 nm3. The center of the box is the center of the two center of masses of two ss-DNA. I want to calculate the 2D distribution of the ions surround the strands in the box. I chose Chain_A, Chain_B and ion as three groups, rather I am