Re: [gmx-users] Failed to lock: md.log.

You can try move md.log to some folder and then copy back such as: 1) mv  md.log /some_folder 2) cp  /some_folder/md.log . It works for me Jianguo - Original Message - From: zhaowh zha...@mail.ustc.edu.cn To: gmx-users gmx-users@gromacs.org; gmx-users gmx-users@gromacs.org;

[gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q

Dear All, Has anyone has Gromacs benchmark on Bluegene/Q? I recently installed gromacs-461 on BG/Q using the following command: cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \   -DGMX_BUILD_OWN_FFTW=ON \ -DBUILD_SHARED_LIBS=OFF \ -DGMX_XML=OFF \

Re: [gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q

? Cheers Jianguo From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Jianguo Li ljg...@yahoo.com.sg Sent: Tuesday, 4 June 2013, 22:32 Subject: Re: [gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q

Re: [gmx-users] keeping water (entirely) out of the bilayer core

Hi Chris, Just think of another possible way without modifying the code. The task can be achieved by increasing the LJ repulsion term between the lipid tail atoms and water molecules, but keeping all other interactions unchanged. To do so, the free energy code can be used. You can create a

Re: [gmx-users] keeping water (entirely) out of the bilayer core

Hi Chris, Perhaps you can try PLUMED+GROMACS. In that case, you can define a collective variable as mindist between the water molecules and the lipid tails. And then apply wall potential to keep this CV above a certain value.  Jianguo From: Christopher

Re: [gmx-users] fail to pull

You switched on the position restraint in your mdp file, is that the reason? From: Albert mailmd2...@gmail.com To: gromacs maillist gmx-users@gromacs.org Sent: Sunday, 7 April 2013, 2:47 Subject: [gmx-users] fail to pull Dear: I am trying to pull my ligand

Re: [gmx-users] Weird result of WHAM

If the two end states of a system are fixed, the free energy difference is independent of the path. I am not sure what caused the problem, but if besides the protein, water and ions, there are some other molecules in your simulation box (e.g., membrane or ligand), the states A and B of your

Re: [gmx-users] steered pulling code on ligand-receptor complex

If you position restraint the receptor or only use several residues at the binding site, in both cases you limit your sampling to a small part of the phase space and the PMF may not be accurate, since the receptor may undergo conformational change upon ligand binding. Cheers --Jianguo -

Re: [gmx-users] Umbrella sampling after TMD of NAMD

It seems difficult to use RMSD as the reaction coordinate to do umbrella sampling simulations. Maybe you can try meta-dynamics in which you can use RMSD as a collective to get the free energy. It is implemented in a modified version of gromacs (GROMETA), or you can use PLUMED together with

Re: [gmx-users] When are .trr files essential? (was: Regarding Gromacs output files)

One situation is the analysis that require velocities, such as calculating velocity autocorrelation function or lateral pressure.  -Jianguo From: Ladasky blind.watchma...@yahoo.com To: gmx-users@gromacs.org Sent: Friday, 12 October 2012, 13:25 Subject:

Re: [gmx-users] Orientation of protein

editconf -princ will put the long axis of the protein in x-direction, after that you may need editconf -rotate 0 90 0 -c to make it in z-direction -Jianguo - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users

Re: [gmx-users] umbrella sampling (PMF) position discrepancy

I guess is that g_wham takes the distance from tpr file which calculates the distance using grommp. It seems that the distances calculated using g_dist and grompp are different, as discussed in this forum about 10 days ago. -Jianguo - Original Message - From: Raphael Alhadeff

Re: [gmx-users] Umbrella Sampling Pull code Problem

I have met similar problem before. The distance calculated by g_dist is different from that calculated by grommp, especially when the actual distance between the two groups is very small. As the actual distance becomes larger, the difference of the distance from the two commands becomes

Re: [gmx-users] Protein-POPC bilayer

After inserting the protein, the equilibrium box length in the x and y dimension should be different, so you need anisotropic pressure coupling during the 1st step. After equilibrium, the ratio of box length in x,y is fixed, so you can use semi-isotropic method. --Jianguo

Re: [gmx-users] Protein-POPC bilayer

the job, but I expect it may take longer time to reach equilibrium. --Jianguo From: Justin Lemkul jalem...@vt.edu To: Jianguo Li ljg...@yahoo.com.sg; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 17 August 2012, 9:19 Subject: Re: [gmx

Re: [gmx-users] how to build a mixed lipid bilayer?

There are several ways, usually I do like the following: 1. first construct one leaflet. Use editconf -translate to construct a small box containing with 3 POPE 1 POPE 2. Use genconf -nbox to replicate the above in x,y dimension to get 64 lipids 3. Use editconf -rotate -translate to get the

Re: [gmx-users] cutting a cylinder from simulation box

Maybe you can try trjorder to order the water molecules around your protein and make a group of those nearest water molecules and output them using trjconv Jianguo From: Sanku M msank...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org

Re: [gmx-users] Free energy between surfaces

One way to get the free energy is to measure the force as a function of distance and do the integration to get the PMF, as used in the paper: Ronen Zangi, Morten Hagen, and B. J. Berne. 2007. Effect of Ions on the Hydrophobic Interaction betweenTwo Plates. J. AM. CHEM. SOC. 2007, 129,

Re: [gmx-users] Water Shell Density

Probably you can use g_rdf -surf to get the surface based g(r) for water molecules, since g(r) is the local_density divided by the average_density, then local_density=g(r)_surf*average_density, which is a function of distance from the surface. Jianguo

Re: [gmx-users] the ligang topology

This paper has used united atoms for -CF3 and -CF2: Hiroaki et al. Enhanced Hydrophobicity of Fluorinated Lipid Bilayer: A Molecular Dynamics Study. J. Phys. Chem. B 2008, 112, 11305–11309. Another way is to use ATB to generate the topology, but I am not sure if it can deal with fluorine

Re: [gmx-users] water channel

You can look at gromacs tool g_flux and g_count at: https://github.com/orbeckst/g_count Jianguo From: Yao Yao ya...@ymail.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Wednesday, 15 February 2012, 10:38 Subject: [gmx-users] water channel Hi

Re: [gmx-users] Orders of the residues in gromacs

Another possible reason is due to vmd, which numbers the residue from 0. Residue 143 in gromacs corresponds to residue 142 in vmd. Cheers, Jianguo From: Du Jiangfeng (BIOCH) j...@maastrichtuniversity.nl To: gmx-users@gromacs.org gmx-users@gromacs.org Sent:

Re: [gmx-users] Failed to lock: md.log. No locks available.

There is a solution in this mailing list sometime before: mv md.log to some other folder and copy it back. Jianguo From: lina lina.lastn...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 13 January 2012, 18:51 Subject:

Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff

which gromacs version are you using? cMAP is implemented in v4.5  or later Jianguo From: César Ávila clav...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, 9 October 2011 12:07 AM Subject: [gmx-users] CMAP for alanine

Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff

: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff To: Jianguo Li ljg...@yahoo.com.sg, Discussion list for GROMACS users gmx-users@gromacs.org Date: Monday, 10 October, 2011, 5:51 PM v4.5.4 As I commented above, I had to manually add an entrance for the cmap terms in the topology file

Re: [gmx-users] Re: about non-writing issue

I met the similar problem before, sometimes my job writes output, sometimes not. My cluster administrator fixed the problem and they told me that there were some problem at some compute nodes which my job unfortunately was dispatched to. Jianguo From: lina

Re: [gmx-users] residue numbering different

The first residue number in VMD is 0, not 1. Jianguo From: aiswarya pawar aiswarya.pa...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 16 September 2011 1:21 PM Subject: [gmx-users] residue numbering different Hi Users,

Re: [gmx-users] how to handle different atom names between pdb and rtp files.

You can either use -ighn option in pdb2gmx or mannualy rename the atom names in the pdb file. Cheers, Jianguo From: KONG Xian xiansh...@gmail.com To: gmx-users@gromacs.org Sent: Tuesday, 13 September 2011 15:36:41 Subject: [gmx-users] how to handle different

Re: [gmx-users] Error when performing grompp on lipid bilayer modeled with CHARMM27

Why not use CHARMM36 FF? It is available in gromacs user contribution website. If I remember correctly, charmm27 cannot yield correct area/lipid, you need to apply surface tension. Cheeers, Jianguo From: Jackson Chief jchief...@gmail.com To:

Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue

you may need to use -ignh option in pdb2gmx. Jianguo From: Kamesh Narasimhan g0701...@nus.edu.sg To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Wednesday, 24 August 2011 14:42:28 Subject: [gmx-users] error:You might need to add atom H to the hydrogen

Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue

-ignh -- I still get the same error. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Jianguo Li [ljg...@yahoo.com.sg] Sent: Wednesday, August 24, 2011 3:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] error:You

Re: [gmx-users] Convert drug Charmm topology to Gromacs

Hi, The .str file contains the information of atomtype, bonds and improper dihedrals, so it is eneough to write a .rtp file. Then using pdb2gmx to generate the itp file. And you also need to add the missing parameters from CgenFF into the itp parameter files based on chapter 5, as Justin

Re: [gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure

Hi, Kong Xian, It is better to use SHAKE instead of LINCS since LINCS does not directly yield pairwise forces, as shown in the paper: Erik Lindahl and Olle Edholm. Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations. JOURNAL OF

[gmx-users] Re: Re：the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure

From: KONG Xian xiansh...@gmail.com To: ljg...@yahoo.com.sg Cc: gmx-users@gromacs.org Sent: Sunday, 21 August 2011 19:20:50 Subject: Re：the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure Thanks for your kindly reply. I used

Re: [gmx-users] Re: local pressure v4.5 issues

Use grompp of v4.0.7 to generate the tpr files using CHARMM FF and give this tpr file to v4.0.2_local_pressure to rerun the simulation. Jianguo From: Amit Choubey kgp.a...@gmail.com To: Jianguo Li ljg...@yahoo.com.sg Cc: Discussion list for GROMACS users

Re: [gmx-users] Re: local pressure v4.5 issues

I have tried CHARMM FF in v4.0.4 and it does not give error, so it seems dihedral type 9 has already been implemented in v4.0.4. Jianguo From: Jianguo Li ljg...@yahoo.com.sg To: Amit Choubey kgp.a...@gmail.com Cc: Discussion list for GROMACS users gmx-users

Re: [gmx-users] How to exert different lateral pressure profile of a membrane to study its influence on a protein inserted in the double layer membrane?

Lateral pressure is a function of z-distance, maybe you can try simulations using different surface tension, which is the integration of lateral pressure. Cheers, Jianguo From: KONG Xian xiansh...@gmail.com To: gmx-users@gromacs.org Sent: Wednesday, 27 July

Re: [gmx-users] REMD with 'bad contacts' error

One thing you can try in your membrane simulation is to couple the Protein, Lipid and Water_Ion separately to the thermal bath. Cheers, Jianguo From: Sheeba Jem sheeba@googlemail.com To: gmx-users@gromacs.org Sent: Wednesday, 6 July 2011 07:05:43

Re: [gmx-users] Energy-groups?

You can specify the energygrps in mdp file, grompp a new tpr file and use -rerun option of the mdrun to get a new edr file Cheers Jianguo From: nishap.pa...@utoronto.ca nishap.pa...@utoronto.ca To: gmx-users@gromacs.org Sent: Tuesday, 7 December 2010

Re: [gmx-users] Re: local pressure v4.5 issues

, did you use CHARMM FF in your simulations and how did you convert the tpr files from v 4.5 to v 4.0? Cheers Jianguo From: Amit Choubey kgp.a...@gmail.com To: Jianguo Li ljg...@yahoo.com.sg; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday

Re: [gmx-users] Re: local pressure v4.5 issues

very much! Cheers, Jianguo From: Amit Choubey kgp.a...@gmail.com To: Jianguo Li ljg...@yahoo.com.sg Cc: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, 1 July 2011 11:47:58 Subject: Re: [gmx-users] Re: local pressure v4.5 issues

Re: [gmx-users] Re: local pressure v4.5 issues

Choubey kgp.a...@gmail.com To: Jianguo Li ljg...@yahoo.com.sg; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 22 June 2011 00:16:43 Subject: Re: [gmx-users] Re: local pressure v4.5 issues On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li ljg...@yahoo.com.sg wrote: Hi Amit, May I

Re: [gmx-users] local pressure calcuation for Gromacs-4.5

Dear all, I have made a test calculation of local pressure using version 4.5 for my membrane simulation using CHARMM FF. When rerun the simulation, mdrun gives the localpressure data. Howeve, instead of giving an anveraged data of the local pressure, mdrun gives a separate file for each frame,

Re: [gmx-users] gmx4.5.4 installation help

The error message already shows some hints. Try recompile FFTW with -fPIC. Jianguo From: Chandan Choudhury iitd...@gmail.com To: gmx-users gmx-users@gromacs.org Sent: Thursday, 2 June 2011 15:03:03 Subject: [gmx-users] gmx4.5.4 installation help Hello

Re: [gmx-users] Gravity force in equation of motion

Seems gravity is much weaker than the other forces in molecular simulations and thus can be neglected. Jianguo From: mohsen ramezanpour ramezanpour.moh...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 1 June 2011

[gmx-users] Improper dihedrals in Charmm FF

Dear all, My molecule contains -CH=CH- fragment and I am trying to create the topology using Charmm FF. It seems that there is no improper dihedrals for -CH=CH- fragment in Charmm FF, while other FF (e.g., Amber or OPLS) has additional improper dihedrals terms for that fragment. Could

Re: [gmx-users] C-terminal amidation of peptide

If you use CHARMM FF and Gromacs4.5 or later, you can use -ter in pdb2gmx and choose CT2 to add NH2 at C-terminus. For other FF, you may need to manually add NH2 in pdb file. Jianguo From: anna Kalkbrenner anna.kalkbren...@gmail.com To:

Re: [gmx-users] Re: g_hbond output

If I understand correctly, $2 is the number of hydrogen bonds defined by cutoff distance and the cutoff angle. $3 is the number of pairs within the cutoff distance, but beyond the cutoff angle. You may got different number of hbonds using different cutoff distance and cutoff angle. Jianguo

Re: [gmx-users] Re: g_hbond output

is my question, since there is already one bond formed, then why there is none pairs in 1000? On Wed, Mar 16, 2011 at 3:16 PM, Jianguo Li ljg...@yahoo.com.sg wrote: If I understand correctly, $2 is the number of hydrogen bonds defined by cutoff distance and the cutoff angle. $3 is the number

Re: [gmx-users] Zero Potential of Mean Force with g_wham

I met the same problem when using 4.5.1 for some systems, the PMF shows zero curve, while the hist file looks fine. The problem disappears when using 4.5.2. Jianguo From: Susana Tomasio susietoma...@gmail.com To: gmx-users@gromacs.org Sent: Wednesday, 9 March

Re: [gmx-users] parallel running

You don't use qsub or bsub? usually you should submit a script file containing the gromacs command, then bsub/qsub will allocate the required resource to your job. Jianguo From: mohsen ramezanpour ramezanpour.moh...@gmail.com To: Discussion list for GROMACS

[gmx-users] REMD simulation of peptide-membrane system

Dear all, I'd like to do folding simulations of a short peptide on membrane surface using REMD using atomistic FF. But the problem is that membrane will disrupt at high temperatures. To maintain the membrane structure, I am thinking the following two methods: (1) To use different coupling

Re: [gmx-users] Re: adding ff parameter of modified residue to charmm ff

My way of doing it is: (1) add two new residues entries (with two different names) for glycine and seine in the rtp file and corresponding FF files. The new entries in the rtp file for glycine and serine should have the same number of atoms as in the real molecule (delete the unnecessary H

Re: [gmx-users] Can g_wham support using different temperature for different windows?

by restraining the peptide in a helical conformation (e.g. 10.1016/j.bpj.2010.12.3682). It is anyway a very difficult problem (and probably impossible at atomistic resolution) to get a converged PMF for a whole peptide (e.g. 10.1016/j.bpj.2009.03.059). Ciao, Patrick Le 23/02/2011 05:25, Jianguo Li

Re: [gmx-users] Can g_wham support using different temperature for different windows?

for GROMACS users gmx-users@gromacs.org Sent: Wednesday, 23 February 2011 20:59:18 Subject: Re: [gmx-users] Can g_wham support using different temperature for different windows? On Feb 23, 2011, at 3:21 AM, Jianguo Li wrote: Thank you  for the the useful information, XAvier. My peptide is highly

Re: [gmx-users] Can g_wham support using different temperature for different windows?

From: Jianguo Li ljg...@yahoo.com.sg To: jalem...@vt.edu; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, 22 February 2011 14:27:34 Subject: Re: [gmx-users] Can g_wham support using different temperature for different windows? Thanks Justin

Re: [gmx-users] Can g_wham support using different temperature for different windows?

windows. Cheers Jianguo From: Justin A. Lemkul jalem...@vt.edu To: Gromacs Users' List gmx-users@gromacs.org Sent: Tuesday, 22 February 2011 21:10:08 Subject: Re: [gmx-users] Can g_wham support using different temperature for different windows? Jianguo Li

Re: [gmx-users] Can g_wham support using different temperature for different windows?

to 8 us ... and no charges were involved. This might be a lot pessimistic but you should not get fooled by a CG model. Martini is really good for a lot of things but other things should really but be looked at carefully. XAvier. On Feb 22, 2011, at 9:12 AM, Jianguo Li wrote: Sorry I forgot

Re: [gmx-users] Can g_wham support using different temperature for different windows?

using different temperature for different windows? Jianguo Li wrote: Thank you, Justin. Actually I did windowed umbrella simulations from d=-1.05nm to d=9nm. Since I think there is no problem in the region out of the membrane, so I only show the configurations within the membrane. My objective

[gmx-users] Can g_wham support using different temperature for different windows?

Dear all, I want to get the PMF of my peptide across the membrane bilayer. First I pulled my peptide across the membrane and then did windowed umbrella sampling along the reaction coordinates which is the z-distance between peptide and membrane. However, I found that sampling is not

Re: [gmx-users] Can g_wham support using different temperature for different windows?

Sent: Tuesday, 22 February 2011 09:58:36 Subject: Re: [gmx-users] Can g_wham support using different temperature for different windows? Jianguo Li wrote: Thanks Justin. I tried your suggestions by either increase more windows and change the force constant, but it seems the samplings are still

Re: [gmx-users] Can g_wham support using different temperature for different windows?

: Tuesday, 22 February 2011 11:13:05 Subject: Re: [gmx-users] Can g_wham support using different temperature for different windows? Jianguo Li wrote: Thanks for your comments, Justin. Using timestep of 20 fs, in each window the simulation runs for 100 ns CG time. The pulling rate is 0.001 nm/ps

Re: [gmx-users] Protein-membrane system

Hi, 3000 water molecule per lipids per second corresponds to 0.000384 water molecules transferred across the membrane per nano second (assume the system contains 128 lipids). It seems water translocation should not be observed in a simulation of 10 ns, but I am not sure. And I only find one

[gmx-users] local pressure calcuation for Gromacs-4.5

Hi All, I found there is a customised version gromacs-4.0.2_localpressure for calculating the local pressure from the Gromacs website. I am wondering is there a higher version? The reason is that I am using CHARMM FF and have done membrane simulations using Gromacs-4.5. If I understand

[gmx-users] box length in z dimension keep increasing when using two walls in NPT ensemble

Dear all, I was trying to add two walls at z=0 and z=z_box to my system which contains one peptide and one membrane. Since I am interested in how the peptides affect membrane properties (i.e., area per lipid), I need to use semi-isotropic pressure coupling. But I wanted to mimick the

[gmx-users] questions about long-range electrostatic interaction in membrane systems

Dear All, I am working on the interaction of a positively charged peptide (18AA) and the bacterial membrane consisting of a mixture of zitterionic and negatively charged lipids. Our experiments show that the peptide can disrutp the membrane. One problem puzzed me is that which method to use