[gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion

ustin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion Message-ID: <28a2dc8e-20e9-abee-4b10-0f3cceb4f...@vt.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 4/23/20 5:42 AM, ABEL Stephane wrote:

[gmx-users] GROMACS mdp file for doing a single point energy after acpype conversion

Deal all, I am using acpype to convert a set of glycolipids modeled with the GLYCAM06 force fiedl into the GROMACS format. acpype works well for this task. But I would like to check if the conversion is correctly done by performing single point energy (SPE) calculations with Amber and

[gmx-users] Some atoms are not properly rotated with gmx_editconf

Hello I would like my gramicidin A channel along the z axis. So I use the following commands in a bash script ## Select a group for determining the system size: System : 0 ## Select group for the determining the orientation ! GramicidinA : 15 ## Select a group that you want to align:

[gmx-users] How to obtain the number of residue per turn with GROMACS ?

Hello, I would like to obtain the time serie of the number of residues per turn with GROMACS for a given peptide ? Is it possible to obtain this property with a GROMACS tool ? If yes, how ? Thank you Stéphane -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Recreating newer TPRs for old Gromacs (Jernej Zidar)

Hello If you only need the parameters of the molecules (e.g. list of bond, atom masses and charges) you could build a fake tpr with a minimal list of parameters (for instance used for minimization) and use an the desired old version of grompp (Gromacs 5.0.3). Stéphane

[gmx-users] Subject: RAM usage of gmx msd5

Hello Did you try to compute the msd for only few atoms (for instance phosphorus), the COM of each lipid or use different segments of your trajectory ? This approach is sometime used. Stéphane -- Message: 2 Date: Tue, 17 Sep 2019 08:46:38 +0200 From: Martin Kern

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 185, Issue 55

Hello Did you try to compute the msd for only few atoms (for instance phosphorus), the COM of each lipid or use different segments of your trajectory ? This approach is sometime used. Stéphane -- Message: 2 Date: Tue, 17 Sep 2019 08:46:38 +0200 From: Martin Kern

[gmx-users] Help with generating Arginine topology for Amber FF (Pandya, Akash)

Hello there are not parameters and RESP charges for standalone residue such as Arg in GROMACS. So you will have to construct a rtp file for this residue and derive the corresponding RESP charges yourself. You could also do a quick in literature to see if some have already done the job for

Re: [gmx-users] Calculating electron density profile of a lipid bilayer system

e into account the number of electrons? I thought that I just need to give the atomic number of each element in the electron.dat file. Could you please give an example on how to modify the number of electrons? Do I need to use the itp file? Thanks a lot. Best regards, Azadeh On Thu, May 30, 2019

Re: [gmx-users] Calculating electron density profile of a lipid bilayer system

Hello I gave you a response few days ago For the calculations of the EDP you have to take into account of the charges of the atom (it is mentioned at the end of density tool ("known issue")) . So modify the number of electrons to have the "real" electron numbers in you electron.dat file

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 181, Issue 64

Hello Azadeh For the calculations of the EDP you have to take into account of the charges of the atom (it is mentioned at the end of density tool ("known issue")) . So modify the number of electrons to have the "real" electron numbers in you electron.dat file accordingly. HTH

Re: [gmx-users] select an atom for "only" residue with make_ndx [ Resolved ]

Thanks Justin it worked. For the record, I have also found that 27 & a C31 C32 C33 is equivalent to a C31 | aC32 | aC33 & rLIPIDC or aC31 | aC32 | aC33 & 27. Note For the two latter commands the order of "r27 or rLIPIDC" is important Thanks again On 5/16/19

[gmx-users] select an atom for "only" residue with make_ndx

selected "all" the C31, C32 and C33 atoms and not only those in the LIPIDC group Stéphane On 5/15/19 11:03 AM, ABEL Stephane wrote: > Hello all, > > I am currently doing simulations of a model of membranes with different types > of lipids (LIPIDA, LIPIDB and LIPIDC) and I

[gmx-users] select an atom for "only" residue with make_ndx

Hello all, I am currently doing simulations of a model of membranes with different types of lipids (LIPIDA, LIPIDB and LIPIDC) and I would like to select a group of atoms for only the same lipid with make_ndx. Below an example Three different lipids : LIPIDA, LIPIDB and LIPIDC contain few

[gmx-users] GROMOS 54A8 Force field

With Google http://vienna-ptm.univie.ac.at/?page_id=100 HTH -- Message: 4 Date: Tue, 7 May 2019 09:14:42 +0200 From: Mark Abraham To: Discussion list for GROMACS users Cc: Discussion list for GROMACS users Subject: Re: [gmx-users] GROMOS 54A8 Force field

[gmx-users] (no subject) (Soham Sarkar)

Hi In your itp you have a "?" ?; GENERATED BY LigParGen Server Remove it and the problem will be solved PS : next time add a title in you message. Good luck - -- Message: 1 Date: Fri, 5 Apr 2019 14:26:00 +0530 From:

Re: [gmx-users] Are the D-CMAP terms present in the last release of CHARMM force field for GROMACS

Thank you Justin, I "grepped" the corresponding atom types. Indeed they are in the cmap files Stéphane -- On 3/5/19 3:33 PM, ABEL Stephane wrote: > Dear all, > > I want to performs some MD simulations of systems with a protein model with >

[gmx-users] Are the D-CMAP terms present in the last release of CHARMM force field for GROMACS (charmm36-nov2018.ff.tgz)?

Dear all, I want to performs some MD simulations of systems with a protein model with D-AA and I would like to have the confirmation that the last release of the CHARMM parameters for GROMACS (i.e. charmm36-nov2018.ff.tgz) contains the D-CMAP terms listed in the

Re: [gmx-users] Dihedral restraints

ive, somehow. Please check your include statements, etc. Mark On Wed., 9 Jan. 2019, 18:05 ABEL Stephane, wrote: > Thanks Mark for your reply > > In the log and edr files I only see an "Position Rest." term. So do you > mean that the contributions on the dihedral restr

Re: [gmx-users] Dihedral restraints

ark On Wed, Jan 9, 2019 at 10:14 AM ABEL Stephane wrote: > Hello > > I would like to apply some dihedral restraints in different residues of my > protein during the production stage. For that I have added at the end of > the protein itp the section > [ dihedral_restrain

[gmx-users] Dihedral restraints

Hello I would like to apply some dihedral restraints in different residues of my protein during the production stage. For that I have added at the end of the protein itp the section [ dihedral_restraints ]. Is it enough ? Should I add something else in the mdp ? In other words, how to be

[gmx-users] Why charge parameter of cations like Cu2+, Zn2+ in GROMOS 54a7 force field in GROMACS equals to zero?

Hi All the the values in the charge column in the ffnonbonded.itp are not used by GROMACS and remain present for history reasons (and probably for compatibility with older GROMACS versions). The charges for each residue/molecules are now in the rtp. Best Stéphane

Re: [gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap [update] and possible bug

n; charset=iso-8859-2; format=flowed On 11/5/18 1:19 PM, ABEL Stephane wrote: > Hello again, > > Does the GROMACS team have some suggestions to help me to resolve my problem > with the output of gmx densmap and xpm2ps to an eps/pdf with all the ticks in > the x/y axis (see below

Re: [gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap [update] and possible bug

-- Message: 2 Date: Sun, 4 Nov 2018 13:19:06 + From: ABEL Stephane To: "gromacs.org_gmx-users@maillist.sys.kth.se" Subject: [gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap [update] and possible bug

[gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap [update] and possible bug

Message: 4 Date: Sat, 3 Nov 2018 17:45:53 +0000 From: ABEL Stephane To: "gromacs.org_gmx-users@maillist.sys.kth.se" Subject: [gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap Message-ID: <3e39b768bb199548ab18f7289e7534af4887a...@exdag0

[gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap

not understand why ... Stéphane -- On 11/3/18 12:19 PM, ABEL Stephane wrote: > Hello, > > I am using the below .m2p file as input for xpm2ps obtained from gmx densmap > (v2018.2), but I am not able to get axis range label. The commands I use for > den

[gmx-users] Regarding xpm2ps with a xpm file obtained from gmx densmap

Hello, I am using the below .m2p file as input for xpm2ps obtained from gmx densmap (v2018.2), but I am not able to get axis range label. The commands I use for densmap and xpm2ps gmx_mpi densmap -f MYXTC.xtc -s MYTPR.tpr -n MYINDEX.ndx -b 15 -e 21 -bin 0.5 -aver z -unit nm-2 -o

[gmx-users] pcoupltype

Just my 2 cents If I recall well CHARMM36 and others force fields (such as lipid14) were initially parametrized and validated using the anisotropic pressure coupling scheme. So it make sense to use it instead of semi-isotropic pressure coupling. Moreover I found that if the membrane system is

[gmx-users] xpm2ps (2018.3) does print axis labels

Sorry for the double post, I resend my message (below) since I have received no response from you guys Hello, I have a problem with gmx xpm2ps (v5.1.4 and 2018.2) with a xpm files generated with gmx_mpi densmap. For example If I use the following xpm

Re: [gmx-users] How to generate a new xtc file with a membrane protein complex properly oriented along a given axis?

, ABEL Stephane wrote: > > Hello All, > > I have basic questions regarding the procedure to generate an new xtc where > a membrane protein inserted a detergent micelle is properly oriented for the > computation of 2D density Map. Indeed for this calculation I need to h

[gmx-users] xpm2ps (2018.3) does print axis labels

Hello, I have a problem with gmx xpm2ps (v5.1.4 and 2018.2) with a xpm files generated with gmx_mpi densmap. For example If I use the following xpm (1) and m2p (2) files and the following command the x and y labels are not plotted in the eps figure. Same behavior problem occurs if I did not

[gmx-users] How to generate a new xtc file with a membrane protein complex properly oriented along a given axis?

Hello All, I have basic questions regarding the procedure to generate an new xtc where a membrane protein inserted a detergent micelle is properly oriented for the computation of 2D density Map. Indeed for this calculation I need to have the protein-surfactant complex properly oriented along

[gmx-users] parameters for plotting 2D density map with gmx densmap and xpm2ps

Dear all, I would like to obtain a 2D density map plot as for instance Fig. 4 in the following paper (DOI 10.1007/s00232-014-9690-8) for a membrane protein inserted in a surfactant micelle with gmx densmap and xpm2ps . I have few questions - Have any of you ever done this type of plot? If

Re: [gmx-users] g_mindist error "Cannot open file with NULL filename string"

://redmine.gromacs.org? Thanks Mark On Tue, Sep 25, 2018 at 3:30 PM ABEL Stephane wrote: > Hi All, > > I would like to use g_mindist (vGMX2018.2) to compute the number of total > contacts between each residue of a protein and surfactant molecules. For > this I use the following co

[gmx-users] g_mindist error "Cannot open file with NULL filename string"

Hi All, I would like to use g_mindist (vGMX2018.2) to compute the number of total contacts between each residue of a protein and surfactant molecules. For this I use the following command gmx_mpi mindist -f myXTC.xtc -s MYPDB.pdb -n MYNDX.ndx -b 20 -e 215000 -dt 4 -d 0.4 -respertime

[gmx-users] minimization is not converging (Bratin Kumar Das)

éphane - Dear ABEL, I tried CHARMM-gui but the charmm gui is getting failed for my system. On Thu, Sep 6, 2018 at 8:50 PM, ABEL Stephane wrote: > Hi > > Did you try to use CHARMM-gui and use the gromacs files generated fo

Re: [gmx-users] minimization is not converging (Bratin Kumar Das)

Hi Did you try to use CHARMM-gui and use the gromacs files generated for this system to see if your problem is resolved? Stéphane -- Message: 5 Date: Thu, 6 Sep 2018 19:55:07 +0530 From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> To: gmx-us...@gromacs.org

[gmx-users] Use different version of tpr in the same simulation... possible ?

Hi there For different reason, I have to use a different version of GROMACS (GMX2016.4) to continue a simulation carried out with GROMACS v2018. Obvioulsy I obtain an error appears about the tpr "reading tpx file version 112 with version 110 program" Is there an alternative to do what I

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 170, Issue 57

mmunication homepage on ScienceDirect ( http://www.sciencedirect.com/science/journal/00104655). Hope that helps. On Thu, Jun 14, 2018 at 5:53 PM ABEL Stephane wrote: > Hi there, > > Do you know where I can find the program g_contacts developed by Christian > Blau & Helmut Grubm

[gmx-users] About the "g_contacts" program for gromacs

Hi there, Do you know where I can find the program g_contacts developed by Christian Blau & Helmut Grubmuller and described in the following paper "g_contacts: Fast contact search in bio-molecular ensemble data. Computer Physics Communications Volume 184, Issue 12, December 2013, Pages

[gmx-users] Speed up simulations with GROMACS with virtual interaction sites

I know the paper but the webpage Thanks you Viveca -- Message: 2 Date: Fri, 6 Apr 2018 16:45:45 +0200 From: Viveca Lindahl To: gmx-us...@gromacs.org Cc: "gromacs.org_gmx-users@maillist.sys.kth.se"

[gmx-users] Speed up simulations with GROMACS with virtual interaction sites

omy, and Genetics University of Oxford From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of ABEL Stephane [stephane.a...@cea.fr] Sent: 06 April 2018 08:51 To: gromacs.org_gmx-users@maillist.sy

[gmx-users] Speed up simulations with GROMACS with virtual interaction sites

Hi gmx users, I know that it is possible to speed up the simulations by a factor 2 (by using a larger timestep) in GROMACS with virtual interaction sites. By I do not find a clear procedure on the web in particular if I use CHARMM. Do you have any pointers or procedures and examples of mdp

[gmx-users] Possible to extract gro file from a tpr?

Hi A quick question here, before to read this response I thought (but never tested) that it was possible to extract a pdb from a tpr since we use one to generate a tpr with grompp. So how is store the atomic coordinates of a system in a tpr file ? Thanks

[gmx-users] Simulation of D-Alanine (prasun kumar)

Hi I added the same problems few days ago.There is no hdb entries for D-AA, so GROMACS can not generate the missing Hs. So I would suggest you to use CHARMM-GUI, instead and use a fake *.itp with the L-ALA (ALA) renamed to DALA. Good luck Stéphane -- Hi Group:

Re: [gmx-users] Missing dihedral parameter (CTD1 C NH1 CT1) for D-AA bonded to L-AA

OK thank you Justin for the confirmation Stéphane -- On 3/9/18 6:55 AM, ABEL Stephane wrote: > Dear all, > > I am constructing a top file for gramicidin A a short that contains a > succession of D- and L-AAs (the exact sequence is > HCO-L-Val-D-Gl

[gmx-users] Missing dihedral parameter (CTD1 C NH1 CT1) for D-AA bonded to L-AA

Dear all, I am constructing a top file for gramicidin A a short that contains a succession of D- and L-AAs (the exact sequence is HCO-L-Val-D-Gly-L-Ala-D-Leu-L-Ala-D-Val-L-Val-D-Val-L-Trp-D-Leu-X-D-Leu-L-Trp-D-Leu-L-Trp-NH-CH2-CH2-OH) and have a unexpected problem whenI use charmm36 . Indeed

Re: [gmx-users] CMAP entries for D-residues with GROMACS (Justin Lemkul)

OK I see thank you, Justin Bye On 3/2/18 10:50 AM, ABEL Stephane wrote: > Dear all, > > I am interested to simulate a system with gramicidin A that contains D-AAs > (D-LEU and D-VaL) and I am wondering if the CMAP entries in the cmap.itp > file (charmm36-jul2017.ff) are used

[gmx-users] CMAP entries for D-residues with GROMACS

Dear all, I am interested to simulate a system with gramicidin A that contains D-AAs (D-LEU and D-VaL) and I am wondering if the CMAP entries in the cmap.itp file (charmm36-jul2017.ff) are used for these types of AA ? I am asking this because I see that the CHARMM force field library

[gmx-users] disulfide bond missing even with -ss

Hi, If your are not sure that SS is formed or taken into account in the top file,. You could do a short minimization of the initial structure and observe the minimized structure has the SS bond. If it also a good way to see if the top file is correct. Sté

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff -- Resolved

<a1922ea9-4776-a450-7bea-5e141850f...@vt.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 1/15/18 12:31 PM, ABEL Stephane wrote: > Hello, > > I have finally resolved my problem thank to Justin . Would you be willing to share the exact sequence of events, commands, etc. th

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff -- Resolved

dified residues with amber ff Message-ID: <b7a10948-61d2-5b3f-b062-6630785c6...@vt.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 1/14/18 12:04 PM, ABEL Stephane wrote: > Thank you, Justin for your interest to my problem, > > But even if I use the -missing argument*

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff

I will try to search a workaround Best Stéphane De : ABEL Stephane Envoy? : dimanche 14 janvier 2018 16:52 ? : gromacs.org_gmx-users@maillist.sys.kth.se Objet : RE:gromacs.org_gmx-users Digest, Vol 165, Issue 50 Thanks Justin First I forgot to say

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff

De : ABEL Stephane Envoyé : dimanche 14 janvier 2018 16:52 À : gromacs.org_gmx-users@maillist.sys.kth.se Objet : RE:gromacs.org_gmx-users Digest, Vol 165, Issue 50 Thanks Justin First I forgot to say that I am building a cyclic peptide (Atosiban, https://fr.wikipedia.org/wiki/Atosiban

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue 50

eptide with two modified residues with amber ff Message-ID: <541ddbd0-378e-16eb-79a4-f161235d4...@vt.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 1/14/18 10:04 AM, ABEL Stephane wrote: > Hi Justin > > I have added the TYO and MER residue as Protein is

Re: [gmx-users] Problem fpr building a peptide with two modified residues with amber ff

Hi Justin I have added the TYO and MER residue as Protein is the residuetypes.dat. And the the following output with pdb2gmx. I select 2 and 6 ## gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes Select

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff

Dear all, I have a peptide with two modified residues at the Nter with the following sequence Mer-TYO-ILE-PHE.GLYNH2. Mer and TYO are a cap and a modified tyrosine residue (side chain), respectively. the Mer, TYR and ILE are bonded together with a peptide bond. To build the corresponding

[gmx-users] Problem with G_WHAM and -bsprof command (Justin Lemkul)

Yeah you are right. It is working now Thank you On 11/20/17 10:18 AM, ABEL Stephane wrote: > hello everybody > > I am trying to obtain the average and SD of PMF profile with gmx wham (gmx > 5.1.2 and 2016.1) with the following command in a bash script > > mpirun

[gmx-users] Problem with G_WHAM and -bsprof command

hello everybody I am trying to obtain the average and SD of PMF profile with gmx wham (gmx 5.1.2 and 2016.1) with the following command in a bash script mpirun -np 1 gmx_mpi wham -it Wham_TPR_step5.dat -if Wham_Pullf_step5.dat -unit kCal -temp 298 -b $begin -e $end -hist

[gmx-users] Conversion Amber to Gromacs

Hello Elisa, "J'arrive après la bataille" To be sure that you have correct Amber parameters for GROMACS, you could also use the acpype suite*. This suite converts Amber params in gromacs format. The program generates the (non)ffbonded.itp and top files in gromacs format from the Amber's LeaP

[gmx-users] problems with difference in the COM distances in US sampling

Hello I am trying to perform some US calculations to obtain the potential of mean force of the insertion of a molecule inside a lipid bilayer. For that I follow the tutorial of Dr Justin Lemkul with some modifications and start the simulations with the following mdp pull_group1_name

[gmx-users] legend in the pulling file (gmx 5.1.4)

Hi all, A quick question: What are the meaniings of the s1 , s1 and s2 legends in the pullf.xvg? @title "Pull COM" @xaxis label "Time (ps)" @yaxis label "Position (nm)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @

[gmx-users] Topolgen and topolbuild

Hi if your molecule is a ligand, you could use ParamChem (https://cgenff.paramchem.org/) Stéphane -- Message: 1 Date: Wed, 4 Oct 2017 10:10:24 +0200 (CEST) From: Sergio Manzetti To: gmx-users

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 162, Issue 9

Hi, In addition to my previous email If you have all the parameters obtained from RESP and tleap program (mol2, frcmod and lib) you could use the ACPYPE program to obtain the itp file for GROMACS See

[gmx-users] Charges and Antechamber

HI It is quite easy to derive RESP charges and use them with GROMACS. You could follow the steps 1) Build a pdb file of your molecule/modified residue 2) Use the web server pyRED (http://upjv.q4md-forcefieldtools.org/REDServer-Development/) and derive the RESP charges. The webserver will

[gmx-users] Necessary files to restart/continue REMD

Hello, Two quick questions about REMD 1) What are the necessatry files to restart a REMD simulations with -append and -noappend arguments? I ask these question because if I do not provide a trr file, GROMACS crashs with a error related to the checksum of the trr 2) Can I use the argument

Re: [gmx-users] -multidir option in REMD (GROMACS v2016.1) -resolved

bra...@gmail.com> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] -multidir option in REMD (GROMACS v2016.1) Message-ID: <camnumaqep0deuo08vqjyvtnpbbd3rjaawa2bd_czh377eea...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Hi, On Wed, Aug 2, 2017 at 11:22 AM ABE

[gmx-users] Error in the replica order in REMD (GMX v2016.1)

Hello again Thanks to J. Hermann I can start my simulations, however few seconds after the beginning of the run I have the following error "Replicas with indices 2 < 12 have temperatures 271.9 > 254.27, please order your replicas on increasing temperature" I do not understand this error,

[gmx-users] -multidir option in REMD (GROMACS v2016.1)

Dear all, I would like to do a REMD of a system with 75 replicas (with 75 directories named md_0,..., md_75) and I have two questions. 1) To launch the md calculation we should use the followng command : mpirun -np 4 mdrun_mpi -v -multidir sim[0123] -replex XXX My question is since I have

[gmx-users] topology servers versus ff

Hello, If you want to use CHARMM for your simulations, do not use PRODRUG to construct your parameters but use ParamChem, instead. https://www.paramchem.org/ Stéphane -- Message: 2 Date: Wed, 12 Jul 2017 14:36:27 +0500 From: maria khan

[gmx-users] topology file with virtual site for an asymetric linear molecule

Dear all, I would like to use the virtual site capability of GROMACS to construct the topology of an asymmetric linear molecule (say SeCN). Does somebody have an example of topology file for a similar molecule to share with me? Thank you Stéphane -- Gromacs Users mailing list * Please

[gmx-users] an error related to Gromacs version

Hello, Probably you used a tpr file does not compatible with an older version of GROMACS. To resolve this problem, you could generate a new tpr with Gromacs 5.0.7 and use it for your free energy calculations HTH -- Message: 4 Date: Sun, 25 Jun 2017 05:05:53

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 49

Hello Xujun >>Could someone give me some suggestion on choosing one typical type of bile >>salts for the study? Which force field is better? You will to read first some biological/physiological textbooks. Moreover, bile salts are complex molecules and probably difficult to model. so I would

[gmx-users] HPC resources in Europe (preferably Northern/Central Europe)

Hello, You could write a proposal to have access to the supercomputers of the PRACE consortium |1]. The access to the machines is free, [1] http://www.prace-ri.eu/ Stéphane -- Message: 3 Date: Mon, 15 May 2017 14:45:00 +0200 From: Jo?o Henriques

[gmx-users] Save the velocities a subset of atoms in a trr file during a simulation

ello, A quick question : It is possible to save the velocities (in a trr file) for only selected atoms "during" a simulation as we can do in case of the xtc files by using a the mdp option compressed-x-grps? Thanks S -- Gromacs Users mailing list * Please search the archive at

[gmx-users] PBC issues with membrane-peptide simulation

Hi, it is not an issue !! To resolve your problem you could simulate two bilayer in box and insert the peptides between them. HTH -- Message: 6 Date: Wed, 9 Nov 2016 16:07:26 +0530 From: Abhi Acharya To:

[gmx-users] problem with backward to construct a CHARMM36 model

Dear all, Sorry in advance if the following message does not follow the netetiquette (my message was already post in the Martini forum) but since more gromacs users read this mailling list than the Martini one, I think that probably some users may help me to resolve my problem. I am

[gmx-users] Reaction Field approach with GROMACS

Hi All, I have a question about the reaction field approach used by GROMACS. I have seen that in earlier version (V.4.6.X andn 4.5.3) there was a bug with the Reaction Field approach (http://redmine.gromacs.org/issues/1400). It is corrected in the GROMACS version than 5.0 or in lastest

[gmx-users] grompp not enough parameters

Hi Marlon, If you change the comma into a point in the force constant values it should work Good luck Hello, I'm trying to use the amber03 ff to simulate a protein with iron clusters. I got the right parameters from a paper but then grompp tells me: "ERROR 1 [file

Re: [gmx-users] top parameters for pluronic f127 (Andrian Saputra)

Hi, Before to compute the partial charges , you have to optimize the molecule. It may be very difficult if you have a large molecule (> 100 atoms). So for polymers with reapeated units, it is always advisable to separate the molecule into similar molecular blocks. It is straighforward for

[gmx-users] Angle between a vector and the normal to a sphere

OK thanks Yu, I have another question how to select the water sphere center dynamically With g_select? S - Hi St?phane, gmx gangle may be what you need. http://manual.gromacs.org/programs/gmx-gangle.html -Yu 2016-05-31 13:22 GMT+02:00 ABEL Stephane

[gmx-users] Angle between a vector and the normal to a sphere

Hi all, Is there a command/tool in a gromacs to compute the angle between a vector defined defined two atoms molecule and the normal to a sphere defined by a set of atoms for instance water ? if yes, how I use a version of gromacs > 5.0 Thanks Stéphane -- Gromacs Users mailing list *

Re: [gmx-users] update .hdb file

Hello Shahla, We have developed a tool for GROMACS (rtp2hdb) that can construct a hdb table file for you with any rtp file. Please contact me contact me off list if you are interested Best -- Message: 5 Date: Sat, 9 Apr 2016 08:49:05 -0400 From: Justin Lemkul

Re: [gmx-users] pdb2gmx error

Indeed Justin I have tried to add the entries for the capped groups in the Amber99SB-ILDN force field (like in the charmm*.ff) since they are not present in aminoacids.n.tdb and aminoacids.c.tdb, so I think I have broken something Stéphane On 4/5/16 6:47 AM, ABEL Stephane 175950 wrote

[gmx-users] empty aminoacids.n.tdb and aminoacids.c.tdb files for Amber99*

Hello again I have noticed that in case of the amber* forcefields (in gromacs v504) the aminoacids.n.tdb and aminoacids.c.tdb files are empty* so it is not possible to construct easily a capped AA with the pdb2gmx -ter command without using a rtp file (and it is very painful). So does anyone

[gmx-users] pdb2gmx error

Hello, When i use pdb2gmx (v.504) and 12 AA long peptide with the Amber99SB-ILDN force field, I have the error : Fatal error: tpA = 53191, i= 0 in print_atoms I have no idea what does this message mean. Could you help me? Thanks -- Gromacs Users mailing list * Please search the archive

[gmx-users] infinite force at the membrane lipid

Hello, How did you construct your membrane, with CHARMM-GUI? What is the lipid? From my experience, I have found that sometimes CHARMM-GUI does not provide a good starting point for MD. So I would suggest you to : - center the lipids inside the box to have no lipids that cross the box limit

[gmx-users] Reverse micelle clustering issue

Hello To center your RM inside teh box you could use to successive trjconv commands with pbc cluster and mol in index.ndx 0 : all 1 AOT 2 water 3 AOT_Water 4 ISO 1 -- select 1 1 0 (or 2 2 0) echo 1 1 0 | trjconv -f my_initial.xtc -s my_tpr.tpr -pbc cluster -ur compact -center -o

[gmx-users] command line with gangle

Hello all, I have a stupid question : I would like to use gangle (v5.0.4) with the following command line gmx_mpi gangle -f conv3.xtc -s 60_SDS_CHARMM_5_NAP_504_run_1.tpr -n paipai_dist_theta.ndx -g1 plane -group1 -g2 plane -group2 -oav test_angle.xvg -b 39000 -e 4 test_angle.txt

[gmx-users] command line with gangle

Many thanks, Teemu it works Stephane -- Message: 3 Date: Fri, 20 Mar 2015 18:05:49 +0200 From: Teemu Murtola teemu.murt...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: Re: [gmx-users] command line with gangle Message-ID:

[gmx-users] how to remove water molecule inside micelle

Hello, It is not a really problem, since the water will move during the simulation (due to the hydrophobic effect), but It may take for that all the water left the micelle center. So I suggest you to use genbox with the following arguments -shell or -vdwd (see the genbox manual). An other

[gmx-users] Naughty Vacuum Bubble in our Vesicle

Hello Bjorn I don't know if it related to your problem, but I see a typo in our mdp file for the pressure coupling: Pcoupltype = isotropic ;semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 4.0 4.0 compressibility

[gmx-users] conversion of the AMBER parameters to GROMACS with negative barrier height values

Hello all, I am trying to convert some GLYCAM parameters to do simulations with the GROMACS code. In the glycam force field, several dihedral terms have negative barrier height values, for instance, -20 in the following parameter: Os-Cj-Cj-Ha 1 -20.00 0.0 2

[gmx-users] Use trjconv in parallel,

Hello, in short : it is possible ? I use the gromacs v4.6.5. Thanks Stéphane -- 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

Re: [gmx-users] Use trjconv in parallel

Thanks for your quick and also fast (;)) reply, Carsten. Stéphane -- Message: 4 Date: Wed, 2 Jul 2014 10:55:45 + From: ABEL Stephane 175950 stephane.a...@cea.fr To: gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se

Re: [gmx-users] Simulations in NVE ensemble with CHARMM36 - update

. The cluster pair list does have a buffering effect, but choosing a larger rlist might be necessary for good energy conservation. Stéphane On 5/7/14, 9:05 AM, ABEL Stephane 175950 wrote: Dear GMX-users I have done a 90 ns long simulation of a heterogeneous system (SPCE water, phospholipids

[gmx-users] Simulations in NVE ensemble with CHARMM36

Dear GMX-users I have done a 90 ns long simulation of a heterogeneous system (SPCE water, phospholipids and a hydrophobic solvent) in NPT ensemble (298 K at 1 bar) with GROMACS4.6.5. to compute related dynamical properties, I would like to continue this simulation in NVE. But I am puzzled to

[gmx-users] conversion xtc to xyz format with openbabel

Hello all, My apologies for these out topic questions Does anybody have already try to convert xtc trajectory into xyz with openbabel? Btw, it seems that pdb file generated with editconf can not be read by openbabel. I obtain the following error : WARNING: Problems reading a PDB file