[gmx-users] Protein potential energy

Dear list, I pulled a protein in water. In order to get the trend of the potential energy terms of the protein, I defined energygrps and reran the system. May I ask can I get the right trend of the protein potential energy terms using this approach? Your help is appreciated. Thanks, Tammy --

[gmx-users] How to perform simulation of carbon nanotube in GROMACS in NPT ensemble?

Dear list, I have gone through carbon nanotube guide on GROMACS website. http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube I have a nanotube aligned to z-direction. I am trying

Re: [gmx-users] How to convert C6 from GROMOS54a7 to sigma for OPLSAA

Hi Justin, thanks for your 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 (un)subscribe requests visit

[gmx-users] How to convert C6 from GROMOS54a7 to sigma for OPLSAA

Dear all, I want to calculate sigma for OPLSAA.ff from C6 developed based on GROMOS54a7.ff. >From the manual, I got the equations: C12 = Sigma^(6)*C6 C6 = 4*sigma^(6)*epsilon However, I found sigma and epsilon are different in OPLSAA and AMBER, and that C6 from GROMOS and sigma from OPLSAA

[gmx-users] g_energy error

Dear list, I want to investigate the trend of the potential energy of the protein in my system with water. I run : trjconv -f md.trr -o protein.xtc tpbconv -s topol.tpr -o protein.tpr mdrun -rerun protein.xtc -s protein.tpr I got the following errors: WARNING: there may be something wrong with

Re: [gmx-users] pulling with constant force

Hi list, I fixed it by setting 'pull-coord1-vec = -1 0 0' Thanks. -- 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 (un)subscribe

[gmx-users] pulling with constant force

Dear list, I want to pull my protein away from each other using a constant force. I fix one end (group 'start') and used the following pull code but found that 2 pulling groups are getting closer no matter whether I set pull-coord1-k as 1000 or -1000. ; COM pulling. pull=

[gmx-users] convert amber topology and coordinates files into gromacs topology

Dear list, I am studying glycoprotein. As amber is very slow on CPUs, I really want to do my simulations in gromacs. I found that gromacs has amber99sb.ff. So I want to convert amber topology and coordinates files into gromacs topology using Antechamber. My concerns are: 1) amber16 has

Re: [gmx-users] is there a way to get pullx.xvg and pullf.xvg from traj_comp.xtc?

Thanks Justin, mdrun -rerun works. But I failed to fix it via gmx traj with this command: gmx traj -f traj_comp.xtc -s topol.tpr -ox pullfx.xvg -of pullf.xvg -dt 400 error say .xtc file do not have force information. Is the command I used correct? -- Gromacs Users mailing list * Please search

[gmx-users] is there a way to get pullx.xvg and pullf.xvg from traj_comp.xtc?

Dear list, I did SMD, but saved the pullx.xvg and pullf.xvg much less frequently compared to the traj_comp.xtc. is it possible to get a more frequently written pull COM coordinates and forces based on the traj_compxtc file I have? Thank you, Ming -- Gromacs Users mailing list * Please search

[gmx-users] is there a way to get pullx.xvg and pullf.xvg from traj_comp.xtc?

Dear list, I did SMD, but saved the pullx.xvg and pullf.xvg much less frequently compared to the traj_comp.xtc. is it possible to get a more frequently written pull COM coordinates and forces based on the traj_compxtc file I have? Thank you -- Gromacs Users mailing list * Please search the

Re: [gmx-users] how to distance between COM of two groups of atoms?

Fixed! Thanks. -- 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 (un)subscribe requests visit

Re: [gmx-users] how to distance between COM of two groups of atoms?

Thank you Justin, I set 2 groups (start and end )in index.ndx file. each group has 3 alpha carbon atoms. I used the following command to calculate the distance between COM of those 2 groups gmx distance -n index.ndx -select 'com of group "start" plus com of group "end"' -f test.pdb -s

[gmx-users] how to distance between COM of two groups of atoms?

Dear list, I found that gmx distance can calculate distance between 2 atoms. is there a way to calculate distance centre of mass between 2 group of atoms? Thanks, Ming -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] hbond between backbone atoms

Dear list, I want to calculate hbond between backbone atoms on different chains of my protein only. but when it give me this error "nothing to be none". I used this command: gxm hbond -f traj.trr -s topol.tpr -num hbnum.xvg -a 30 -r 0.5 I can use this command to get hbond between protein and

[gmx-users] how to order gpus on different nodes

Dear experts, I can order 2 gpus on one node from HPC using the following script: #PBS -l select=1:ncpus=2:ngpus=2:mpiprocs=2:mem=2gb mpiexec_mpt -n 2 gmx_mpi mdrun -v -deffnm npt -nb gpu -gpu_id 01 -ntomp 2 however when I used the following script to order 4 gpus on 2 nodes, it gave me an

[gmx-users] GPUs performance on Gromacs calculation

Dear experts, I did SMD on 2 M2090 GPUs and 16 CPUs on one node. The simulation ran around 500 steps every 15 minutes. However, the SMD simulation ran around 68000 steps using 96 CPUs without GPU. Is this because the M2090 GPU type works badly on Gromacs? Our Uni has the following types of GPU.

Re: [gmx-users] bond_atomtype

Thank you Justin, SI in ffnonbonded.itp is correct. -- 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 (un)subscribe requests visit

[gmx-users] bond_atomtype

Dear list, I want to add parameters for silicon in oplsaa.ff In .rtp I added: [ SI ] [ atoms ] SI opls_966 4.000 0 In .atp I added: opls_966 28.08000 ; Si In ffnonbonded.itp I added: opls_966 Si4+ 1428.08000 4.000 A4.43500e-01 3.98000e-01

Re: [gmx-users] pdb2gmx generate .itp file for each molecule

Hi , Maybe you can try -merge all when using pdb2gmx. -- 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 (un)subscribe requests visit

Re: [gmx-users] confusion on energy for a system of protein sovated in water

Thanks Justin, How about LJ and Coulomb energy? I want to see the trend of protein energy only. I defined 2 energy group: protein and SOL in .mdp file. Then, I saw LJ and Coulomb: protein-ptrotein option when using g_energy. Are they VDW and Coulomb force within the protein only? --

[gmx-users] confusion on energy for a system of protein sovated in water

Dear lists, After pulling a protein in water and performing mdrun -rerun, I found that G96Bond, G96Angle, COM-Pull-En and Potential energy extracted from the original system using g_energy -f ener.edr , and from the -rerun system using g_energy -f rerun.edr have different values. Firstly, are

Re: [gmx-users] fix COM

Hi Mark, When I submitted my job to our HPC sever, I got this error message: gromacs/5.0.4(14):ERROR:151: Module 'gromacs/5.0.4' depends on one of the module(s) '' gromacs/5.0.4(14):ERROR:102: Tcl command execution failed: prereq mpt/2.10 I have been told that the mpt version has been updated

Re: [gmx-users] fix COM

Thank you Mark, Could you please help to give more instructions on how to generate restraints on a centre of mass virtual site? I know genrestr can implement restraints, but I have no idea how to set a virtual site. BTW: is the latest version suitable for mpt 2.13? it seems that version

Re: [gmx-users] fix COM

Hi Justin, Thanks for your information. My atom group contains only 3 atoms, each of which is on one chain of a triple helix. Flat-bottomed is new for me. I went through section 4.3.2 in the manual, but still feel confused about how to get the parameters and how to apply constraints. Do you

[gmx-users] fix COM

Dear Gromacs experts, Is there a approach to fix the centre of mass of a group of atoms only without fixing all of the atoms during a stretching process? Regards, Ming -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] the helical axis of a triple helix

Dear list, I want to calculate the trajectory of the helical axis of a triple helix. Do you have any suggestions for me to achieve this? Any suggestions is appreciated. Thanks, Ming -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Weird configuration when pulling rate is small

Dear Erik, Thanks for your advice. I think you are right. However, when using -pbc whole, every chain is intact but the three chains separate in some frames; when using -pbc nojump, the collagen molecule is not intact (there is a small part stay in the other box ) either. If I fix one end, and

[gmx-users] Weird configuration when pulling rate is small

Dear list, I am pulling a triple helix using umbrella distance. When the pulling rate is 0.0004 nm/ps, the configuration is normal. However, when I decrease the pulling rate to 0.0002 nm/ps or lower, the configuration is messy (some atoms flow away from the triple helix), but the simulations

Re: [gmx-users] weird configuration when pulling rate is small

Hi Tsjerk, I tried, and got the same configuration. Initially, I add -nojump when using g_traj. I am not sure whether it has something to do with the pulling method (umbrella distance). In reference, researchers use SMD (fix the COM of one group, and stretch the COM of the other group). But I

[gmx-users] weird configuration when pulling rate is small

Dear list, I am pulling a triple helix using umbrella distance. When the pulling rate is 0.0004 nm/ps, the configuration is normal. However, when I decrease the pulling rate to 0.0002 nm/ps or lower, the configuration is messy (some atoms flow far away), but the simulations run well and the

[gmx-users] difference between entropic energy and free energy

Deer list, I am quite confused about the concept of entropic energy and free energy. Could anybody help to tell me what is the difference between them? Thanks. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] A question about simulation system includes more than 100000 atoms using Gromacs

my system includes1,700,000 atoms, and runs well with 5.0.4. Sent from my Huawei Mobile 张竹青 zhuqingzh...@ucas.ac.cn wrote: Dear Madam/Sir, I have recently tried to use Gromacs to simulation a biolmoleculal system including more than 10 atoms. As usually, the .gro file just supports the

Re: [gmx-users] LJ-14 energy

...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Thursday, 16 July 2015 9:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] LJ-14 energy On 7/16/15 7:08 AM, Ming Tang wrote: Dear Justin, Thanks. 1. The total Lennar-Jones 12-6 energy of the whole system is the addition of LJ-14, LJ-SR

Re: [gmx-users] LJ-14 energy

- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Thursday, 16 July 2015 11:20 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] LJ-14 energy On 7/15/15 8:39 PM, Ming Tang wrote: Dear

[gmx-users] LJ-14 energy

Dear Gromacs experts, I am confused about the meaning of LJ-14 option in g_energy. I checked the achieve, and found that Justin said it stands for intramolecular interactions between atoms separated by 3 bonds. My simulation is protein solvated in water. How can I calculate the Lennard-Jones

Re: [gmx-users] [gm.-users] LJ-14 energy

: Re: [gmx-users] LJ-14 energy On 7/15/15 5:27 AM, Ming Tang wrote: Dear Gromacs experts, I am confused about the meaning of LJ-14 option in g_energy. I checked the achieve, and found that Justin said it stands for intramolecular interactions between atoms separated by 3 bonds. My simulation

[gmx-users] LJ-14 energy

] On Behalf Of Justin Lemkul Sent: Wednesday, 15 July 2015 11:36 PM To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org Subject: Re: [gmx-users] LJ-14 energy On 7/15/15 5:27 AM, Ming Tang wrote: Dear Gromacs experts, I am confused about the meaning of LJ-14 option in g_energy. I

Re: [gmx-users] difference between steep and cg

Subject: Re: [gmx-users] difference between steep and cg Hi Ming Tang, See https://en.m.wikipedia.org/wiki/Gradient_descent It has a further link to CG. Cheers, Tsjerk On Jul 11, 2015 4:10 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear Gromacs experts, I am quite confused about the difference

Re: [gmx-users] restrain COM of a group of atoms

: [gmx-users] restrain COM of a group of atoms I do now know what authors meant. However, the COM-COM pulling implies that one group is restrained and another group moves relative to it. So, the COM of the reference group is already fixed in the pull code. On Sun, Jul 5, 2015 at 4:02 AM, Ming

[gmx-users] difference between steep and cg

Dear Gromacs experts, I am quite confused about the difference between the energy minimization algorithm steep and cg. According to my experience, MPI is not suitable for cg. Sometimes, even if the system has already converged using steep algorithm, it can be further minimized if one changes

[gmx-users] restrain COM of a group of atoms

Dear Gromacs experts and users, I am here to seek help. I want to use constraint pull method to pull a filament. My plan is to keep the center of mass of one group fixed through a stiff restraint, say 3×10e5, and pull the other group. I tried to generate the restraint .itp file and modify the

[gmx-users] how to define wall-atomtype?

Dear all, I want to pull a collagen in NPT using direction-periodic, and have to use pbc=xy with wall. I checked both manual and .mdp options and searched mailing lists regarding wall definition in google, but am still have no idea how to define wall-atomtype. I want to use 12-6 wall type.

Re: [gmx-users] confusion on NPT MD simulation

on NPT MD simulation On 6/18/15 6:28 AM, Ming Tang wrote: Dear Tsjerk and Justin, Thanks for your help. I have tried to use 1000 and 1 to restrained the whole protein during NPT equilibration, but found the protein shape changed as well. Is position restraint compatible with pressure

Re: [gmx-users] confusion on NPT MD simulation

Dear Justin, I tried again, and the position restraint works well in NPT equilibration. Thanks very much. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Ming Tang Sent: Friday, 19 June

Re: [gmx-users] confusion on NPT MD simulation

: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Wednesday, 17 June 2015 1:53 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] confusion on NPT MD simulation Hi Ming Tang, You don't

Re: [gmx-users] confusion on NPT MD simulation

...@gromacs.org Subject: Re: [gmx-users] confusion on NPT MD simulation On 6/16/15 5:27 AM, Ming Tang wrote: Dear Justin, I read a paper, in which the author equilibrated the collagen like this: Firstly, a 100 ps NVT MD simulation at a temperature 310 K was performed, in which velocity

Re: [gmx-users] confusion on NPT MD simulation

] On Behalf Of Ming Tang Sent: Monday, 15 June 2015 6:05 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] confusion on NPT MD simulation Dear Justin, I got a problem making me confused for weeks. I found 2 journals, in which the author kept parts of their protein to equilibrate their system in NPT

Re: [gmx-users] confusion on NPT MD simulation

2015 9:46 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] confusion on NPT MD simulation On 6/1/15 4:40 AM, Ming Tang wrote: Dear gromacs experts, I tried to equilibrate a triple helix using NPT, and the .mdp file is like this: DEFINE = -DPOSRES integrator = md dt

Re: [gmx-users] g_wham error in umbrella simulation

Hi，高 发银行卡号给我，我还你钱，你结婚肯定要用钱吧 Sent from my Huawei Mobile Ming Tang m21.t...@qut.edu.au wrote: Dear all, I am doing an umbrella simulation, and come across the following error. Command line: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 Found 27 tpr and 27 pull

Re: [gmx-users] gmx distance

June 2015 11:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gmx distance On 6/5/15 9:49 PM, Ming Tang wrote: Thanks, Justin Using -pbc or not gives the same curve. I tried to guess the curve give the deviation of the two end groups, but the curve drops from around 4nm to 1nm

[gmx-users] gmx distance

Dear gromacs experts, I am stretching a triple helix along z direction by fixing one end and pull the other. The helix length changes from 35nm to 50nm during the MD simulation. However, after using gmx distance -n index.ndx -f traj.trr -s topol.tpr -select 'com of group start plus com of

[gmx-users] g_helix issue

Dear all, I am using gromos54a7 ff to simulate a triple helix. When using g_helix to get some of the basic properties, I got the following error: Program g_helix, VERSION 5.0.4 Source code file: /home/tm/Downloads/gromacs/src/gromacs/gmxana/hxprops.c, line: 437 Fatal error: Zero complete

Re: [gmx-users] fix COM of a group

of a group Hi Ming Tang, You didn't tell you were pulling... That's a totally different matter. I guess you want to use two pull groups and pull one with respect to the other. Cheers, Tsjerk On Wed, Jun 3, 2015 at 11:20 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear Tsjerk, Thanks for your

Re: [gmx-users] fix COM of a group

Of Tsjerk Wassenaar Sent: Wednesday, 3 June 2015 5:41 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] fix COM of a group Hi Ming Tang, comm_mode = Linear comm_grps = CA Cheers, Tsjerk On Wed, Jun 3, 2015 at 9:34 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear all

[gmx-users] fix COM of a group

Dear all, Is there any method that can fix the center of mass of a group of atoms? I create a group containing CA atoms of the first residue in each of the three chains, and want to fix its center of mass only without freeze the CA atoms. Thanks. -- Gromacs Users mailing list * Please search

[gmx-users] does gromos force field support implicit solvent?

Dear gromacs experts, I tried to use gromos 54a7 force field to calculate persistence length of a helix in implicit solvent, but got GB parameters missing errors. When I tried to modify the implicit_genborn_params section, I found there is not gbsa.itp file in gromos54a7.ff does gromos force

[gmx-users] confusion on NPT MD simulation

Dear gromacs experts, I tried to equilibrate a triple helix using NPT, and the .mdp file is like this: DEFINE = -DPOSRES integrator = md dt = 0.0009 nsteps = 100 nstxout = 0 nstvout = 0 nstlog = 1 nstxtcout

[gmx-users] persistence length of triple helix

Dear all, I want to calculate the persistence length of a triple helix. After minimization and equilibration, I did MD simulation without position restraints for atoms. I read the second paragraph of gmx polystat, and understood that for one chain, I can choose its backbone atoms as the index

Re: [gmx-users] first residue in chains warning issue

...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Saturday, 23 May 2015 6:24 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] first residue in chains warning issue On 5/22/15 3:39 AM, Ming Tang wrote: Dear Justin

Re: [gmx-users] first residue in chains warning issue

:39 AM, Ming Tang wrote: Dear Justin, After minimization, I got the following note when using NPT. NOTE 1 [file topol.top, line 49]: The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has an estimated oscillational period of 1.0e-02 ps, which is less than 10 times

Re: [gmx-users] water box moves during MD simulation

of these for doing the simulation, and any of these for representing the trajectory afterwards. Mark On Wed, May 20, 2015 at 11:19 AM Ming Tang m21.t...@qut.edu.au wrote: Dear Brother， What does Mark mean？ Sent from my Huawei Mobile Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Nothing wrong

Re: [gmx-users] Pull code

] On Behalf Of Justin Lemkul Sent: Thursday, 23 April 2015 10:33 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Pull code On 4/22/15 8:03 PM, Ming Tang wrote: Hi, Justin I am confusing about what is the difference between the rigid constraint in constraint pull method and the harmonic

[gmx-users] distance constrain of two groups

Dear all, After energy minimization, I want to equilibrate my triple helix using NPT, but need to keep its general shape, as I want to study the load-deformation relationship including the triple helix unfolding stage. During the equilibration, I want to fix the distance between the centre of

[gmx-users] water box moves during MD simulation

Dear all, After MD dynamic simulation for 100 ps, I found the water box was moving during the simulation, but my protein was inside the water box all the time. Here is the . mdp file I used: integrator = md dt = 0.001 nsteps = 10 nstxout = 1000

Re: [gmx-users] water box moves during MD simulation

of equivalent representations, so mdrun suits itself. Mark On Wed, May 20, 2015 at 9:05 AM Ming Tang m21.t...@qut.edu.au wrote: Dear all, After MD dynamic simulation for 100 ps, I found the water box was moving during the simulation, but my protein was inside the water box all the time. Here

Re: [gmx-users] first residue in chains warning issue

...@gromacs.org Subject: Re: [gmx-users] first residue in chains warning issue On 5/18/15 7:39 AM, Ming Tang wrote: Dear Justin, After minimization, I got the following note when using NPT. NOTE 1 [file topol.top, line 49]: The bond in molecule-type Protein_chain_A between atoms 1 N and 2

Re: [gmx-users] energy minimization problem

Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10:14, Ming Tang m21.t

Re: [gmx-users] energy minimization problem

[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Sunday, 17 May 2015 7:07 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/16/15 8:30 AM, Ming Tang wrote: Dear Justin, I tried to use small time step. First, set dt=0.005ps

Re: [gmx-users] energy minimization problem

Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, That's pretty quick. I guess that this is on multiple cores, given the size of the system. It often helps to equilibrate on a limited number of cores, but I'm not sure that's feasible. Did you obtain the model by martinizing

Re: [gmx-users] energy minimization problem

May 2015 6:47 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, That's pretty quick. I guess that this is on multiple cores, given the size of the system. It often helps to equilibrate on a limited number of cores, but I'm not sure that's

Re: [gmx-users] energy minimization problem

not know whether it is true or not, as the small triple helix used for test does not carry charge, so I did not add CL. Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Ming Tang

Re: [gmx-users] energy minimization problem

...@maillist.sys.kth.se] On Behalf Of Tsjerk Wassenaar Sent: Monday, 18 May 2015 6:21 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] energy minimization problem Hi Ming Tang, Can you run in NVT? Then afterwards you can try NPT without position restraints. Cheers, Tsjerk On May 18, 2015 10

Re: [gmx-users] first residue in chains warning issue

...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Tuesday, 12 May 2015 10:19 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] first residue in chains warning issue On 5/12/15 8:10 AM, Ming Tang wrote: Thanks Justin, At first

Re: [gmx-users] energy minimization problem

Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be reasonable according to gromacs website. So ijust kept trying 0.02ps Sent from my Huawei Mobile Justin Lemkul jalem...@vt.edu wrote: On 5/14/15 10:02 PM, Ming Tang wrote: Hi Justin Here is the .mdp file with position

Re: [gmx-users] energy minimization problem

] On Behalf Of Justin Lemkul Sent: Friday, 15 May 2015 2:40 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] energy minimization problem On 5/14/15 3:12 AM, Ming Tang wrote: Dear all, I am working with a triple helix containing around 1000 amino acids per chain using martini force field

[gmx-users] martini issues

Dear all, I am learning martini method in gromacs through the tutorial http://md.chem.rug.nl/cgmartini/index.php/proteins.http://md.chem.rug.nl/cgmartini/index.php/proteins when solvating the system, I came across the following note: NOTE: This file uses the deprecated 'group' cutoff_scheme.

[gmx-users] Martini CG water

Dear all, I am trying to learn simulation in gromacs 5.0.4 using martini force field, when learning the tutorial (http://md.chem.rug.nl/cgmartini/index.php/proteins) step by step, I got the following note when doing gmx slovate: NOTE: This file uses the deprecated 'group' cutoff_scheme. This

Re: [gmx-users] first residue in chains warning issue

Thanks. EM and NPT run without any warnings. Sent from my Huawei Mobile Justin Lemkul jalem...@vt.edu wrote: On 5/12/15 8:10 AM, Ming Tang wrote: Thanks Justin, At first, I wanted to choose NONE in for both N and C terminus, but it gave me the same warnings for both the first

Re: [gmx-users] HYL force field

: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Monday, 11 May 2015 9:41 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] HYL force field On 5/10/15 10:12 PM, Ming Tang wrote: Hi, 范聪 I have never

[gmx-users] first residue in chains warning issue

Dear all, I built a triple helix with 2 GLN and 1 SER being the first residue of the three chains. However, while using pdb2gmx -f 1.pdb -o complex.gro -ignh -ter -ff gromos54a7 -water SPC and choosing NH2 or NH3+ as the start terminus type for GLN-1 and SER-1, I came across the following

Re: [gmx-users] HYL force field

:39:39, Ming Tang m21.t...@qut.edu.au wrote: Dear all, I want to simulate a protein containing hydroxylysine (HYL). I checked all the force fields, but no .rtp file includes the parameters of it. How can I derive it correctly? Thanks. -- Gromacs Users mailing list * Please search the archive

[gmx-users] How to use pdb2gmx be used to convert PRO to HYP?

Hi，Justin I have been told by an author of one journsl that pdb2gmx can convert PRO to HYP while generating. I did not find the option. Can you give me some advice. Thanks Sent from my Huawei Mobile Justin Lemkul jalem...@vt.edu wrote: On 4/30/15 6:46 AM, vidhya sankar wrote: Dear justin

Re: [gmx-users] How to use pdb2gmx be used to convert PRO to HYP?

: Re: [gmx-users] How to use pdb2gmx be used to convert PRO to HYP? On 4/30/15 9:57 AM, Mark Abraham wrote: Hi, Please do everyone the courtesy of starting a new email, rather than replying to a digest and confusing the archive and email readers. On Thu, Apr 30, 2015 at 3:50 PM Ming Tang m21

Re: [gmx-users] 회신: Re: Generating topology file containing HYP

AM To: gmx-us...@gromacs.org Subject: [gmx-users] 회신: Re: Generating topology file containing HYP Dear Ming Tang I am also using free version. To concert proline to hydroxypropine, 1. Read your pdb file using discovery studio visualizer 2. You will find there is list of menu in the left side

Re: [gmx-users] How to use pdb2gmx be used to convert PRO to HYP?

at 3:50 PM Ming Tang m21.t...@qut.edu.au wrote: Hi，Justin I have been told by an author of one journsl that pdb2gmx can convert PRO to HYP while generating. I did not find the option. Can you give me some advice. Get knowledgeable reviewers ;-) You can't do it with pdb2gmx. Some building

Re: [gmx-users] Generating topology file containing HYP

file containing HYP Dear Ming Tang As long as I know, Discovery studio visualizer can do the mutation from proline to hydroxyproline in a simple way. Hope it helps, Sangeun Jee On Wed, Apr 29, 2015 at 5:42 AM, Ming Tang m21.t...@qut.edu.au wrote: Dear all, I have a pdb file, and need

[gmx-users] Generating topology file containing HYP

Dear all, I have a pdb file, and need to convert some of the proline to hydroxyproline. Can I use pdb2gmx to convert proline to hydroxyproline when generating the topology file? If I cannot, then which kind of software can be used to convert proline to hydroxyproline when generating the

Re: [gmx-users] trjconv for cutting the trajectory in small subtrajectories

Hi，-e is end frame， -b is the start one. Sent from my Huawei Mobile Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi GMx user I simulated protein-ligand comolex with gromacs. total simulation time is 20ns. when I use trjconv for cutting the trajectory in small subtrajectories from

Re: [gmx-users] Pull code

in the new version. Is that the case? Thanks, Alex On Wed, Apr 22, 2015 at 5:58 PM, Ming Tang m21.t...@qut.edu.au wrote: Hi, Alex I tried this code plus freeze all of the atoms in the group needed to stay in place, and it worked well. -Original Message- From: gromacs.org_gmx-users-boun

Re: [gmx-users] g_wham error in umbrella simulation

2015 10:18 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] g_wham error in umbrella simulation On 4/22/15 4:46 AM, Ming Tang wrote: Hi, Justin Thanks a lot. Dos2unix works. There is even no blank space in every line. The problem is that I downloaded those .dat files from the internet

[gmx-users] Problems in the modelling of interaction between peptide and copper

Dear all, I got a problem when modelling the interaction of a peptide and copper. I am using the force field of opls-aa. The charge of copper atoms are defined as zero and the non-bonded parameters are obtained from the CU ions, which can be found in opls-aa. I applied smd and found that the

Re: [gmx-users] Pull code

Hi， Justin I will try whether i can set reference group using umbrella later. Sent from my Huawei Mobile Justin Lemkul jalem...@vt.edu wrote: On 4/22/15 7:17 PM, Ming Tang wrote: Hi，Alex You can try constraint. In umbrella， both 2 groups move. Not really. The constraint option keeps

Re: [gmx-users] Pull code

: [gmx-users] Pull code On 4/22/15 7:17 PM, Ming Tang wrote: Hi，Alex You can try constraint. In umbrella， both 2 groups move. Not really. The constraint option keeps a rigid constraint between the two groups. The umbrella keyword specifies a harmonic potential, whose strength is tunable

Re: [gmx-users] Pull code

Hi, Alex I tried this code plus freeze all of the atoms in the group needed to stay in place, and it worked well. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Alex Sent: Thursday, 23

Re: [gmx-users] Pull code

Hi，Alex You can try constraint. In umbrella， both 2 groups move. Sent from my Huawei Mobile Alex nedoma...@gmail.com wrote: Hi all, I have a group (DNA) I'd like to translate relative to the other group (CNT) along the Z-direction so that DNA is the only group that's actually moving. The

Re: [gmx-users] g_wham error in umbrella simulation

in umbrella simulation On 4/19/15 9:53 PM, Ming Tang wrote: Dear all, I am doing an umbrella simulation, and come across the following error. Command line: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 Found 27 tpr and 27 pull force files in tpr-files.dat and pullf

Re: [gmx-users] g_wham error in umbrella simulation

Thanks for your advice. I just checked. There is no empty line at the end of the .dat files. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Kortzak, Daniel Sent: Monday, 20 April 2015

[gmx-users] g_wham error in umbrella simulation

Dear all, I am doing an umbrella simulation, and come across the following error. Command line: g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 2000 Found 27 tpr and 27 pull force files in tpr-files.dat and pullf-files.dat, respectively Reading 13 tpr and pullf files

Re: [gmx-users] force field problem....

Hi, Justin Thank you so much. I should be much more cautious in the future. there is another interesting thing. why doesn't it give the warning regarding mismatching between CLA and CL when I use MG in the pdb and topol file? I did not copy CN88. actually, I typed it. I got those 2 parameters

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